GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcvP in Pseudomonas fluorescens FW300-N2E3

Align glycine dehydrogenase [decarboxylating]; EC 1.4.4.2 (characterized)
to candidate AO353_08720 AO353_08720 glycine dehydrogenase

Query= CharProtDB::CH_003480
         (957 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_08720
          Length = 957

 Score = 1258 bits (3255), Expect = 0.0
 Identities = 633/957 (66%), Positives = 753/957 (78%), Gaps = 8/957 (0%)

Query: 4   TLSQLENSGAFIERHIGPDAAQQQEMLNAVGAQSLNALTGQIVPKDIQLATPPQVGAPAT 63
           +LSQL +  AF+ RH+GPD A+QQ ML+++G  S   L  Q VP  I+L     +     
Sbjct: 6   SLSQLRDPNAFLRRHLGPDTAEQQAMLDSLGLGSRVELIEQTVPPGIRLNRVLDLPPALD 65

Query: 64  EYAALAELKAIASRNKRFTSYIGMGYTAVQLPPVILRNMLENPGWYTAYTPYQPEVSQGR 123
           E AALA+L+  A +N+ +TS IGMGY     P VILRN+LENPGWYTAYTPYQPE++QGR
Sbjct: 66  EEAALAKLRGYAEQNQVWTSLIGMGYHGTLTPAVILRNVLENPGWYTAYTPYQPEIAQGR 125

Query: 124 LEALLNFQQVTLDLTGLDMASASLLDEATAAAEAMAMAKRVSKLKNANRFFVASDVHPQT 183
           LEALLNFQQ+T+DLTGL++A+ASLLDEATAAAEAMA+AKRV+K K+ N FFV  + HPQT
Sbjct: 126 LEALLNFQQLTIDLTGLELANASLLDEATAAAEAMALAKRVAKSKS-NLFFVDENCHPQT 184

Query: 184 LDVVRTRAETFGFEVIVDDAQKVLDHQDVFGVLLQQVGTTGEIHDYTALISELKSRKIVV 243
           + VV+TRAE FGFE+IVD    +  HQ VFG LLQ   T G+I D   LI  L +++ + 
Sbjct: 185 ISVVKTRAEGFGFELIVDTVDNLKQHQ-VFGALLQYPDTHGDIRDLRPLIDHLHAQQALA 243

Query: 244 SVAADIMALVLLTAPGKQGADIVFGSAQRFGVPMGYGGPHAAFFAAKDEYKRSMPGRIIG 303
            VAAD+++L+LLT PG+ GAD+VFGS+QRFGVPMGYGGPHAAFFA++DE+KR++PGRIIG
Sbjct: 244 CVAADLLSLLLLTPPGEMGADVVFGSSQRFGVPMGYGGPHAAFFASRDEFKRAIPGRIIG 303

Query: 304 VSKDAAGNTALRMAMQTREQHIRREKANSNICTSQVLLANIASLYAVYHGPVGLKRIANR 363
           VSKDA GN ALRMA+QTREQHIRREKANSNICT+QVLLANIAS YAVYHGP GLKRIA R
Sbjct: 304 VSKDARGNVALRMALQTREQHIRREKANSNICTAQVLLANIASFYAVYHGPQGLKRIAQR 363

Query: 364 IHRLTDILAAGLQQKGLKLRHAHYFDTLCVEVA-DKAGVLTRAEAAEINLRSDILNAVGI 422
           +HRLT ILAAGL++ G+   + H+FDTL +EV   +  ++  A+AA+INLR      VG+
Sbjct: 364 VHRLTCILAAGLERNGITRLNQHFFDTLTLEVGGSQTAIIDSAKAAQINLRILGRGQVGL 423

Query: 423 TLDETTTRENVMQLFNVLLGDNHGLDIDTLDKDVAHDSRSIQPAMLRDDEILTHPVFNRY 482
           +LDE+     V +LF+V LG +HGLD+  LD +       I  ++LR    L HPVFN +
Sbjct: 424 SLDESCDERTVAKLFDVFLGADHGLDVAELDGEPLVSG--IPESLLRTTSYLRHPVFNAH 481

Query: 483 HSETEMMRYMHSLERKDLALNQAMIPLGSCTMKLNAAAEMIPITWPEFAELHPFCPPEQA 542
           HSETEM+RY+  LE KDLALNQ+MIPLGSCTMKLNA++EMIPITWP FA LHPF P EQA
Sbjct: 482 HSETEMLRYLKQLENKDLALNQSMIPLGSCTMKLNASSEMIPITWPAFANLHPFAPKEQA 541

Query: 543 EGYQQMIAQLADWLVKLTGYDAVCMQPNSGAQGEYAGLLAIRHYHESRNEGHRDICLIPA 602
            GY  MI++L  WL  +TG+DA+CMQPNSGAQGEYAGLLAIR YHESR +G RDICLIPA
Sbjct: 542 VGYSLMISELESWLCAITGFDAICMQPNSGAQGEYAGLLAIRKYHESRQQGARDICLIPA 601

Query: 603 SAHGTNPASAHMAGMQVVVVACDKNGNIDLTDLRAKAEQAGDNLSCIMVTYPSTHGVYEE 662
           SAHGTNPASA MAGM+V++V CD  GN+DL DL+AKA  AGD LSC+M TYPSTHGVYEE
Sbjct: 602 SAHGTNPASAQMAGMRVMIVDCDDAGNVDLDDLKAKATAAGDKLSCLMATYPSTHGVYEE 661

Query: 663 TIREVCEVVHQFGGQVYLDGANMNAQVGITSPGFIGADVSHLNLHKTFCIPHGGGGPGMG 722
            I E+CEV+H  GGQVY+DGAN+NAQVG+  P  IGADVSH+NLHKTFCIPHGGGGPGMG
Sbjct: 662 GISEICEVIHSHGGQVYMDGANLNAQVGLARPADIGADVSHMNLHKTFCIPHGGGGPGMG 721

Query: 723 PIGVKAHLAPFVPGHSVVQIEGMLTRQGAVSAAPFGSASILPISWMYIRMMGAEGLKKAS 782
           PIGV+AHLAPFV  H VV IEG   + GAVSAAP+GSASILPISWMYI MMG + L  AS
Sbjct: 722 PIGVRAHLAPFVANHPVVPIEGPHPQNGAVSAAPWGSASILPISWMYIAMMGPQ-LADAS 780

Query: 783 QVAILNANYIASRLQDAFPVLYTGRDGRVAHECILDIRPLKEETGISELDIAKRLIDYGF 842
           +VAIL+ANY+A  L  AFPVLYTGR+ RVAHECILD+RPLK +TGISE D+AKRL+DYGF
Sbjct: 781 EVAILSANYLAKHLSGAFPVLYTGRNERVAHECILDLRPLKAQTGISEEDVAKRLMDYGF 840

Query: 843 HAPTMSFPVAGTLMVEPTESESKVELDRFIDAMLAIRAEIDQVKAGVWPLEDNPLVNAPH 902
           HAPTMSFPV GTLMVEPTESESK ELDRFI AML+IRAEI +V+ G W  EDNPL  +PH
Sbjct: 841 HAPTMSFPVPGTLMVEPTESESKAELDRFISAMLSIRAEIAEVQNGNWSAEDNPLKRSPH 900

Query: 903 IQSELVAEWAHPYSREVAVFPAGVA--DKYWPTVKRLDDVYGDRNLFCSCVPISEYQ 957
             +++   W  PYS E AV P       KYWPTV R+D+VYGDRNLFC+CVP+ EY+
Sbjct: 901 TLADITGVWDRPYSIEQAVTPDAHTRLHKYWPTVNRVDNVYGDRNLFCACVPVDEYR 957


Lambda     K      H
   0.319    0.134    0.395 

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: 2315
Number of extensions: 83
Number of successful extensions: 7
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: 957
Length of database: 957
Length adjustment: 44
Effective length of query: 913
Effective length of database: 913
Effective search space:   833569
Effective search space used:   833569
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 AO353_08720 AO353_08720 (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.14230.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 1536.8   0.0          0 1536.6   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720  AO353_08720 glycine dehydrogenas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720  AO353_08720 glycine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1536.6   0.0         0         0       1     939 []      19     950 ..      19     950 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1536.6 bits;  conditional E-value: 0
                                     TIGR00461   1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkv 65 
                                                   rhlGpd+aeq+ ml++lG  +  +lieq vp+ irl+r l l+ +  e +ala+l+  a++n++ 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720  19 RHLGPDTAEQQAMLDSLGLGSRVELIEQTVPPGIRLNRVLDLPPALDEEAALAKLRGYAEQNQVW 83 
                                                   9**************************************************************** PP

                                     TIGR00461  66 ksyiGkGyyatilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanas 130
                                                   +s iG+Gy +t++p vi+rn+lenpgwytaytpyqpei+qGrleallnfq++++dltGle+anas
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720  84 TSLIGMGYHGTLTPAVILRNVLENPGWYTAYTPYQPEIAQGRLEALLNFQQLTIDLTGLELANAS 148
                                                   ***************************************************************** PP

                                     TIGR00461 131 lldegtaaaeamalsfrvskkkankfvvakdvhpqtlevvktraeplgievivddaskvkkavdv 195
                                                   llde+taaaeamal++rv+k+k+n f+v++++hpqt++vvktrae +g+e+ivd ++++k++ +v
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720 149 LLDEATAAAEAMALAKRVAKSKSNLFFVDENCHPQTISVVKTRAEGFGFELIVDTVDNLKQH-QV 212
                                                   *****************************************************999888876.6* PP

                                     TIGR00461 196 lGvllqypatdGeildykalidelksrkalvsvaadllaltlltppgklGadivlGsaqrfGvpl 260
                                                   +G+llqyp t+G+i d++ lid+l+ ++al +vaadll+l lltppg++Gad+v+Gs+qrfGvp+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720 213 FGALLQYPDTHGDIRDLRPLIDHLHAQQALACVAADLLSLLLLTPPGEMGADVVFGSSQRFGVPM 277
                                                   ***************************************************************** PP

                                     TIGR00461 261 GyGGphaaffavkdeykrklpGrivGvskdalGntalrlalqtreqhirrdkatsnictaqvlla 325
                                                   GyGGphaaffa++de+kr +pGri+Gvskda Gn alr+alqtreqhirr+ka+snictaqvlla
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720 278 GYGGPHAAFFASRDEFKRAIPGRIIGVSKDARGNVALRMALQTREQHIRREKANSNICTAQVLLA 342
                                                   ***************************************************************** PP

                                     TIGR00461 326 nvaslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtltvevgekaasevlkaa 390
                                                   n+as yavyhGp+Glk+ia+r++rlt ilaagl+r++    n+++fdtlt+evg   + ++  +a
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720 343 NIASFYAVYHGPQGLKRIAQRVHRLTCILAAGLERNGITRLNQHFFDTLTLEVGGSQT-AIIDSA 406
                                                   *****************************************************98777.788999 PP

                                     TIGR00461 391 eeaeinlravvltevgialdetttkedvldllkvlagkdnlglsseelsed.vansfpaellrdd 454
                                                   ++a+inlr +  ++vg++lde+  ++ v +l++v++g d +gl++ el+ + + + +p+ llr+ 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720 407 KAAQINLRILGRGQVGLSLDESCDERTVAKLFDVFLGAD-HGLDVAELDGEpLVSGIPESLLRTT 470
                                                   *************************************87.********98725568********* PP

                                     TIGR00461 455 eilrdevfnryhsetellrylhrleskdlalnqsmiplGsctmklnataemlpitwpefaeihpf 519
                                                    +lr++vfn +hsete+lryl++le+kdlalnqsmiplGsctmklna+ em+pitwp fa++hpf
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720 471 SYLRHPVFNAHHSETEMLRYLKQLENKDLALNQSMIPLGSCTMKLNASSEMIPITWPAFANLHPF 535
                                                   ***************************************************************** PP

                                     TIGR00461 520 apaeqveGykeliaqlekwlveitGfdaislqpnsGaqGeyaGlrvirsyhesrgeehrniclip 584
                                                   ap eq+ Gy  +i++le+wl+ itGfdai++qpnsGaqGeyaGl +ir+yhesr+++ r+iclip
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720 536 APKEQAVGYSLMISELESWLCAITGFDAICMQPNSGAQGEYAGLLAIRKYHESRQQGARDICLIP 600
                                                   ***************************************************************** PP

                                     TIGR00461 585 asahGtnpasaamaGlkvvpvkcdkeGnidlvdlkakaekagdelaavmvtypstyGvfeetire 649
                                                   asahGtnpasa+maG++v+ v+cd+ Gn+dl dlkaka  agd+l+++m typst+Gv+ee+i e
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720 601 ASAHGTNPASAQMAGMRVMIVDCDDAGNVDLDDLKAKATAAGDKLSCLMATYPSTHGVYEEGISE 665
                                                   ***************************************************************** PP

                                     TIGR00461 650 vidivhrfGGqvyldGanmnaqvGltspgdlGadvchlnlhktfsiphGGGGpgmgpigvkshla 714
                                                   +++++h+ GGqvy+dGan+naqvGl++p+d+Gadv+h+nlhktf+iphGGGGpgmgpigv++hla
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720 666 ICEVIHSHGGQVYMDGANLNAQVGLARPADIGADVSHMNLHKTFCIPHGGGGPGMGPIGVRAHLA 730
                                                   ***************************************************************** PP

                                     TIGR00461 715 pflpktdlvsvvelegesksigavsaapyGsasilpisymyikmmGaeGlkkasevailnanyla 779
                                                   pf+ +   + vv +eg + + gavsaap+Gsasilpis+myi+mmG++ l  asevail+anyla
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720 731 PFVAN---HPVVPIEGPHPQNGAVSAAPWGSASILPISWMYIAMMGPQ-LADASEVAILSANYLA 791
                                                   *****...88999**********************************8.99************** PP

                                     TIGR00461 780 krlkdaykilfvgrdervahecildlrelkekagiealdvakrlldyGfhaptlsfpvaGtlmve 844
                                                   k l  a+++l++gr+ervahecildlr+lk+++gi+++dvakrl+dyGfhapt+sfpv+Gtlmve
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720 792 KHLSGAFPVLYTGRNERVAHECILDLRPLKAQTGISEEDVAKRLMDYGFHAPTMSFPVPGTLMVE 856
                                                   ***************************************************************** PP

                                     TIGR00461 845 ptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqslivaewadpysreeaay 909
                                                   pteses+ eldrfi am++i++ei +v++G++++edn+lk +ph+l + i++ w  pys e+a+ 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720 857 PTESESKAELDRFISAMLSIRAEIAEVQNGNWSAEDNPLKRSPHTLAD-ITGVWDRPYSIEQAVT 920
                                                   ********************************************8875.9*************** PP

                                     TIGR00461 910 papvlkyfkfwptvarlddtyGdrnlvcsc 939
                                                   p + ++ +k+wptv+r+d++yGdrnl+c+c
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720 921 PDAHTRLHKYWPTVNRVDNVYGDRNLFCAC 950
                                                   *****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (939 nodes)
Target sequences:                          1  (957 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: 0.05u 0.03s 00:00:00.08 Elapsed: 00:00:00.08
# Mc/sec: 10.18
//
[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