GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcvP in Paraburkholderia bryophila 376MFSha3.1

Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate H281DRAFT_02409 H281DRAFT_02409 glycine dehydrogenase

Query= reanno::pseudo6_N2E2:Pf6N2E2_5558
         (953 letters)



>FitnessBrowser__Burk376:H281DRAFT_02409
          Length = 978

 Score = 1280 bits (3313), Expect = 0.0
 Identities = 640/955 (67%), Positives = 765/955 (80%), Gaps = 16/955 (1%)

Query: 11  FIARHIGPRASDEQAMLERLGYDSLEALSASVIPESIKGTSVLDMG---DGQSEADALAS 67
           F  RHIGP A+D++AMLE LG+ S  AL  +VIP++I+ T  L +G     +SEA+ALA+
Sbjct: 26  FAERHIGPDAADQEAMLEALGFTSRAALIDAVIPKTIRRTEPLPLGPFAQPKSEAEALAA 85

Query: 68  IKAIAAKNQLFKTYIGQGYYNCHTPAPILRNLLENPAWYTAYTPYQPEISQGRLEALLNF 127
           ++ +A KNQ+F++YIGQGYYN HTP  ILRN+LENPAWYTAYTPYQPEISQGRLEALLNF
Sbjct: 86  LRELADKNQVFRSYIGQGYYNAHTPTVILRNVLENPAWYTAYTPYQPEISQGRLEALLNF 145

Query: 128 QTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSNAFFASVHSHPQTLDVLRTR 187
           Q +I DLTGL I+NASLLDEATAAAEAMT  +R+ K K SN FF +    PQT++V++TR
Sbjct: 146 QQMIVDLTGLAISNASLLDEATAAAEAMTLLQRVGKPK-SNVFFVADDVLPQTIEVVKTR 204

Query: 188 AEPLGIDVVVGDERELSDVSGFFGALLQYPASNGDLFDYRELTERFHTANALVAVAADLL 247
           A P+GI+V VG   E ++ + F G LLQYP  NGD+ DYR LTE  H A   V VAADLL
Sbjct: 205 ATPVGIEVKVGPAAEAANANAF-GVLLQYPGVNGDVRDYRALTEAIHAAGGHVVVAADLL 263

Query: 248 ALTLLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVGVSVDRFG 307
           ALT+LTPPGE+GADVA+G+ QRFGVP+GFGGPHAAY + +D FKR MPGRLVGV+VD  G
Sbjct: 264 ALTVLTPPGEWGADVAVGNTQRFGVPVGFGGPHAAYLAVRDEFKRQMPGRLVGVTVDAQG 323

Query: 308 KPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLVQIANRIHHLTAI 367
            PALRLA+QTREQHIRREKATSN+CTAQ LLA +ASMYAVYHGP+GL  IA R++ + A+
Sbjct: 324 NPALRLALQTREQHIRREKATSNVCTAQALLAIMASMYAVYHGPRGLKTIALRVNRIAAL 383

Query: 368 LAKGLGALGLSVEQESFFDTLTLRTGAQTAALHDKARAQRINLRVVDAERLGLSLDETTS 427
           LA+G   LG ++  E+FFDTLT  TGA+T ALHD A+A+RINLR V   ++G+S+DETTS
Sbjct: 384 LAEGAKQLGYTLVNETFFDTLTFDTGARTQALHDAAKAKRINLRRVSDTQVGVSIDETTS 443

Query: 428 QADVEALLRLIGNLMADGKAVPDF----AALAASVQSHIPAELVRQSAILSHPVFNRYHS 483
           + D+  LL +     A  K  P      AA+ AS  + +PA L R SA L+H VFNR+HS
Sbjct: 444 RRDLGDLLAVFAQA-AGAKDAPQVDTLDAAITASSTASVPAALERTSAYLTHHVFNRHHS 502

Query: 484 ETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAG 543
           ETE++RYLR L+DKDLALDR+MIPLGSCTMKLNA SEM+PVTW EFG +HPFAPAEQ+ G
Sbjct: 503 ETEMLRYLRSLSDKDLALDRSMIPLGSCTMKLNATSEMLPVTWPEFGQIHPFAPAEQTVG 562

Query: 544 YQQLTDELEAMLCAATGYDAVSLQPNAGSQGEYAGLLAIRAYHQSRGEDRRDICLIPSSA 603
           Y+++ D+LE ML AATGY AVSLQPNAGSQGEYAGLL I AYH SRGE  R++CLIP+SA
Sbjct: 563 YREMIDQLEEMLVAATGYAAVSLQPNAGSQGEYAGLLIIHAYHASRGEAHRNVCLIPASA 622

Query: 604 HGTNPATAHMAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGI 663
           HGTNPA+A MAGM+VVV ACDA+GNVD+EDL+ KA +H + LAA+MITYPSTHGVFE+ +
Sbjct: 623 HGTNPASAQMAGMQVVVVACDAQGNVDVEDLKKKADQHADKLAAIMITYPSTHGVFEQNV 682

Query: 664 REICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPI 723
           REIC I+H  GGQVY+DGANMNAMVGL APG+FGGDVSHLNLHKTFCIPHGGGGPGVGP+
Sbjct: 683 REICEIVHARGGQVYVDGANMNAMVGLTAPGQFGGDVSHLNLHKTFCIPHGGGGPGVGPV 742

Query: 724 GVKSHLAPFLPGHASMERKQ-----GAVCAAPFGSASILPITWMYIRMMGGAGLKRASQL 778
            V +HLAPFLP   S   ++     GAV  AP+GSASILPI+WMYI MMG   L  A++ 
Sbjct: 743 AVGAHLAPFLPNQISSGYERAPNGIGAVSGAPYGSASILPISWMYIAMMGAKNLTAATET 802

Query: 779 AILNANYIARRLEEHYPVLYSGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHA 838
           AILNANY+A++L  HYPVLYSG  GLVAHECILDLRP+K++SGI+VDDVAKRL D+GFHA
Sbjct: 803 AILNANYVAKKLAPHYPVLYSGPGGLVAHECILDLRPIKETSGITVDDVAKRLADYGFHA 862

Query: 839 PTMSFPVAGTLMIEPTESESKEELDRFCDAMICIREEIRAVENGSLDKDDNPLKNAPHTA 898
           PTMSFPV GTLM+EPTESESKEELDRF +AMI IR EIRAVE G  D++DNPLK+APHTA
Sbjct: 863 PTMSFPVPGTLMVEPTESESKEELDRFIEAMIAIRNEIRAVEEGRSDREDNPLKHAPHTA 922

Query: 899 AEIVG-EWTHPYSREQAVYPVASLIDGKYWPPVGRVDNVFGDRNLVCACPSIESY 952
           A ++  EW H Y+RE A YP+ +LI  KYWPPVGR DNV+GDRNL C+C  +  Y
Sbjct: 923 AVVIADEWKHAYARETAAYPLPTLIAKKYWPPVGRADNVYGDRNLFCSCVPVADY 977


Lambda     K      H
   0.319    0.135    0.398 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 2260
Number of extensions: 90
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 953
Length of database: 978
Length adjustment: 44
Effective length of query: 909
Effective length of database: 934
Effective search space:   849006
Effective search space used:   849006
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (26.6 bits)

Align candidate H281DRAFT_02409 H281DRAFT_02409 (glycine dehydrogenase)
to HMM TIGR00461 (gcvP: glycine dehydrogenase (EC 1.4.4.2))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR00461.hmm
# target sequence database:        /tmp/gapView.16529.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00461  [M=939]
Accession:   TIGR00461
Description: gcvP: glycine dehydrogenase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                    Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
          0 1475.4   0.1          0 1475.3   0.1    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_02409  H281DRAFT_02409 glycine dehydrog


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_02409  H281DRAFT_02409 glycine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1475.3   0.1         0         0       1     939 []      29     971 ..      29     971 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1475.3 bits;  conditional E-value: 0
                                    TIGR00461   1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkle...apakeyealaelkkiasknk 63 
                                                  rh+Gpd+a+q+ ml++lGf +  ali+ ++pk ir + pl l+    p++e eala l+++a+kn+
  lcl|FitnessBrowser__Burk376:H281DRAFT_02409  29 RHIGPDAADQEAMLEALGFTSRAALIDAVIPKTIRRTEPLPLGpfaQPKSEAEALAALRELADKNQ 94 
                                                  9***************************************9973324677**************** PP

                                    TIGR00461  64 kvksyiGkGyyatilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevana 129
                                                  +++syiG+Gyy++ +p vi+rn+lenp wytaytpyqpeisqGrleallnfq++++dltGl ++na
  lcl|FitnessBrowser__Burk376:H281DRAFT_02409  95 VFRSYIGQGYYNAHTPTVILRNVLENPAWYTAYTPYQPEISQGRLEALLNFQQMIVDLTGLAISNA 160
                                                  ****************************************************************** PP

                                    TIGR00461 130 slldegtaaaeamalsfrvskkkankfvvakdvhpqtlevvktraeplgievivddaskvkkavdv 195
                                                  sllde+taaaeam l +rv k k+n f+va+dv pqt+evvktra p+giev v+ a +  +  + 
  lcl|FitnessBrowser__Burk376:H281DRAFT_02409 161 SLLDEATAAAEAMTLLQRVGKPKSNVFFVADDVLPQTIEVVKTRATPVGIEVKVGPAAEAAN-ANA 225
                                                  *******************************************************9999776.578 PP

                                    TIGR00461 196 lGvllqypatdGeildykalidelksrkalvsvaadllaltlltppgklGadivlGsaqrfGvplG 261
                                                  +Gvllqyp+ +G++ dy+al+++++     v vaadllalt+ltppg+ Gad+++G +qrfGvp+G
  lcl|FitnessBrowser__Burk376:H281DRAFT_02409 226 FGVLLQYPGVNGDVRDYRALTEAIHAAGGHVVVAADLLALTVLTPPGEWGADVAVGNTQRFGVPVG 291
                                                  ****************************************************************** PP

                                    TIGR00461 262 yGGphaaffavkdeykrklpGrivGvskdalGntalrlalqtreqhirrdkatsnictaqvllanv 327
                                                  +GGphaa++av+de+kr++pGr+vGv+ da+Gn+alrlalqtreqhirr+katsn+ctaq+lla +
  lcl|FitnessBrowser__Burk376:H281DRAFT_02409 292 FGGPHAAYLAVRDEFKRQMPGRLVGVTVDAQGNPALRLALQTREQHIRREKATSNVCTAQALLAIM 357
                                                  ****************************************************************** PP

                                    TIGR00461 328 aslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtltvevgekaasevlkaaeea 393
                                                  as+yavyhGp+Glk ia r+ r++++la g k+ +y l n+t+fdtlt + g ++  ++  aa+++
  lcl|FitnessBrowser__Burk376:H281DRAFT_02409 358 ASMYAVYHGPRGLKTIALRVNRIAALLAEGAKQLGYTLVNETFFDTLTFDTGARTQ-ALHDAAKAK 422
                                                  ****************************************************9987.9******** PP

                                    TIGR00461 394 einlravvltevgialdetttkedvldllkvlagkd..nlglsseelsedvan....sfpaellrd 453
                                                   inlr v  t+vg+++dett+++d+ dll v+a     + + ++++l+  ++     s+pa+l+r+
  lcl|FitnessBrowser__Burk376:H281DRAFT_02409 423 RINLRRVSDTQVGVSIDETTSRRDLGDLLAVFAQAAgaKDAPQVDTLDAAITAsstaSVPAALERT 488
                                                  ********************************87541133456778887766555679******** PP

                                    TIGR00461 454 deilrdevfnryhsetellrylhrleskdlalnqsmiplGsctmklnataemlpitwpefaeihpf 519
                                                  + +l+++vfnr+hsete+lryl +l  kdlal++smiplGsctmklnat emlp+twpef++ihpf
  lcl|FitnessBrowser__Burk376:H281DRAFT_02409 489 SAYLTHHVFNRHHSETEMLRYLRSLSDKDLALDRSMIPLGSCTMKLNATSEMLPVTWPEFGQIHPF 554
                                                  ****************************************************************** PP

                                    TIGR00461 520 apaeqveGykeliaqlekwlveitGfdaislqpnsGaqGeyaGlrvirsyhesrgeehrniclipa 585
                                                  apaeq+ Gy+e+i qle+ lv  tG+ a+slqpn+G+qGeyaGl +i  yh srge hrn+clipa
  lcl|FitnessBrowser__Burk376:H281DRAFT_02409 555 APAEQTVGYREMIDQLEEMLVAATGYAAVSLQPNAGSQGEYAGLLIIHAYHASRGEAHRNVCLIPA 620
                                                  ****************************************************************** PP

                                    TIGR00461 586 sahGtnpasaamaGlkvvpvkcdkeGnidlvdlkakaekagdelaavmvtypstyGvfeetirevi 651
                                                  sahGtnpasa+maG++vv+v+cd +Gn+d++dlk+ka++++d+laa+m+typst+Gvfe+ +re++
  lcl|FitnessBrowser__Burk376:H281DRAFT_02409 621 SAHGTNPASAQMAGMQVVVVACDAQGNVDVEDLKKKADQHADKLAAIMITYPSTHGVFEQNVREIC 686
                                                  ****************************************************************** PP

                                    TIGR00461 652 divhrfGGqvyldGanmnaqvGltspgdlGadvchlnlhktfsiphGGGGpgmgpigvkshlapfl 717
                                                  +ivh  GGqvy+dGanmna vGlt+pg++G dv+hlnlhktf+iphGGGGpg+gp++v +hlapfl
  lcl|FitnessBrowser__Burk376:H281DRAFT_02409 687 EIVHARGGQVYVDGANMNAMVGLTAPGQFGGDVSHLNLHKTFCIPHGGGGPGVGPVAVGAHLAPFL 752
                                                  ****************************************************************** PP

                                    TIGR00461 718 pktdlvsvvelegesksigavsaapyGsasilpisymyikmmGaeGlkkasevailnanylakrlk 783
                                                  p+ ++ s    e   + igavs apyGsasilpis+myi+mmGa+ l+ a+e ailnany+ak+l 
  lcl|FitnessBrowser__Burk376:H281DRAFT_02409 753 PN-QISSG--YERAPNGIGAVSGAPYGSASILPISWMYIAMMGAKNLTAATETAILNANYVAKKLA 815
                                                  *9.56654..4556789************************************************* PP

                                    TIGR00461 784 daykilfvgrdervahecildlrelkekagiealdvakrlldyGfhaptlsfpvaGtlmveptese 849
                                                   +y++l+ g  + vahecildlr++ke +gi + dvakrl dyGfhapt+sfpv+Gtlmveptese
  lcl|FitnessBrowser__Burk376:H281DRAFT_02409 816 PHYPVLYSGPGGLVAHECILDLRPIKETSGITVDDVAKRLADYGFHAPTMSFPVPGTLMVEPTESE 881
                                                  ****************************************************************** PP

                                    TIGR00461 850 sleeldrfidamiaikeeidavkaGeiklednilknaphslqslivaewadpysreeaaypapvlk 915
                                                  s+eeldrfi+amiai++ei av +G+ + edn+lk aph++  +i+ ew+++y+re aayp+p l 
  lcl|FitnessBrowser__Burk376:H281DRAFT_02409 882 SKEELDRFIEAMIAIRNEIRAVEEGRSDREDNPLKHAPHTAAVVIADEWKHAYARETAAYPLPTLI 947
                                                  ****************************************************************** PP

                                    TIGR00461 916 yfkfwptvarlddtyGdrnlvcsc 939
                                                    k+wp v+r d++yGdrnl+csc
  lcl|FitnessBrowser__Burk376:H281DRAFT_02409 948 AKKYWPPVGRADNVYGDRNLFCSC 971
                                                  ************************ PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (939 nodes)
Target sequences:                          1  (978 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.06u 0.02s 00:00:00.08 Elapsed: 00:00:00.07
# Mc/sec: 12.75
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory