GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcvP in Shewanella loihica PV-4

Align glycine dehydrogenase [decarboxylating]; EC 1.4.4.2 (characterized)
to candidate 5210634 Shew_3062 glycine dehydrogenase (RefSeq)

Query= CharProtDB::CH_003480
         (957 letters)



>FitnessBrowser__PV4:5210634
          Length = 962

 Score = 1325 bits (3430), Expect = 0.0
 Identities = 643/961 (66%), Positives = 787/961 (81%), Gaps = 6/961 (0%)

Query: 2   TQTLSQLENSGAFIERHIGPDAAQQQEMLNAVGAQSLNALTGQIVPKDIQLATPPQVGAP 61
           T+TL+QLE    FI RHIGPD+A QQEMLN VGA+SL  LT QIVP+ I+L     VG+ 
Sbjct: 3   TETLTQLEQHELFIRRHIGPDSADQQEMLNFVGAESLEDLTQQIVPESIRLGRDLAVGSA 62

Query: 62  ATEYAALAELKAIASRNKRFTSYIGMGYTAVQLPPVILRNMLENPGWYTAYTPYQPEVSQ 121
             E   LA ++  A +NK F SYIGMGY    +P VI RN+ ENPGWYTAYTPYQPE++Q
Sbjct: 63  CGEAEGLASIRKYADKNKVFKSYIGMGYYGTIVPSVIQRNVFENPGWYTAYTPYQPEIAQ 122

Query: 122 GRLEALLNFQQVTLDLTGLDMASASLLDEATAAAEAMAMAKRVSKLKNANRFFVASDVHP 181
           GRLEA+LNFQQ+++DLTGLD+ASASLLDEATAAAEAMA+AKRVSK K AN FF+A DV P
Sbjct: 123 GRLEAILNFQQLSMDLTGLDLASASLLDEATAAAEAMALAKRVSKAKKANIFFIADDVFP 182

Query: 182 QTLDVVRTRAETFGFEVIVDDAQKVLDHQDVFGVLLQQVGTTGEIHDYTALISELKSRKI 241
           QT+DVV+TRAE FGFE++V  A + ++++ +FG L Q     G+I D+T L + L+ +K 
Sbjct: 183 QTIDVVKTRAECFGFEIVVGPASEAVNYE-LFGALFQYTNHYGQITDFTELFAALQEKKA 241

Query: 242 VVSVAADIMALVLLTAPGKQGADIVFGSAQRFGVPMGYGGPHAAFFAAKDEYKRSMPGRI 301
           VV+VAADIM+LV L +PG  GAD+VFGSAQRFGVPMG+GGPHAAFF  +D++KRS+PGRI
Sbjct: 242 VVTVAADIMSLVSLKSPGSMGADVVFGSAQRFGVPMGFGGPHAAFFVTRDQHKRSLPGRI 301

Query: 302 IGVSKDAAGNTALRMAMQTREQHIRREKANSNICTSQVLLANIASLYAVYHGPVGLKRIA 361
           IGVS+D  GN ALRMAMQTREQHIRREKANSNICT+QVLLAN+AS YAV+HGP GLK IA
Sbjct: 302 IGVSQDTRGNRALRMAMQTREQHIRREKANSNICTAQVLLANMASFYAVFHGPQGLKIIA 361

Query: 362 NRIHRLTDILAAGLQQKGLKLRHAHYFDTLCVEVADKAGVLTRAEAAEINLRSDILNAVG 421
           +RIHRL DI AAGL+ KG++L +  +FDT+  +VAD A    RA A E+NLR D    +G
Sbjct: 362 DRIHRLADIFAAGLKAKGVELVNNTWFDTVSFKVADSAAAQARAIAGEVNLRIDSDGILG 421

Query: 422 ITLDETTTRENVMQLFNVLLGDNHGLDIDTLDKDV-AHDSRSIQPAMLRDDEILTHPVFN 480
           + + ETTTRE+V QLF+++LG+ HGLD+  +D D+ A+ S SI   ++R D IL HP FN
Sbjct: 422 VAMAETTTREDVAQLFDIVLGEGHGLDVAAIDADIIANGSNSIPAELVRQDAILEHPTFN 481

Query: 481 RYHSETEMMRYMHSLERKDLALNQAMIPLGSCTMKLNAAAEMIPITWPEFAELHPFCPPE 540
           RYHSETEMMRY+  LE KDLALN +MI LGSCTMKLNAA EM+P++WPEF  +HPFCP +
Sbjct: 482 RYHSETEMMRYIKRLENKDLALNHSMISLGSCTMKLNAATEMMPVSWPEFGNMHPFCPQD 541

Query: 541 QAEGYQQMIAQLADWLVKLTGYDAVCMQPNSGAQGEYAGLLAIRHYHESRNEGHRDICLI 600
           QA+GY ++I +L++WLV +TGYDA+CMQPNSGA GEYAGLLAI+ YHESR EGHR++CLI
Sbjct: 542 QAQGYAELIEELSNWLVDITGYDAMCMQPNSGASGEYAGLLAIKKYHESRGEGHRNVCLI 601

Query: 601 PASAHGTNPASAHMAGMQVVVVACDKNGNIDLTDLRAKAEQAGDNLSCIMVTYPSTHGVY 660
           P SAHGTNPASA +AGM++VV ACDK GN+D+ DL+AKA +  +NLSCIMVTYPSTHGVY
Sbjct: 602 PQSAHGTNPASAQLAGMKIVVTACDKQGNVDMEDLKAKAAEVAENLSCIMVTYPSTHGVY 661

Query: 661 EETIREVCEVVHQFGGQVYLDGANMNAQVGITSPGFIGADVSHLNLHKTFCIPHGGGGPG 720
           EETI E+CEV+HQ GGQVYLDGANMNAQVG+TSPG IGADVSHLNLHKTF IPHGGGGPG
Sbjct: 662 EETISEICEVIHQHGGQVYLDGANMNAQVGLTSPGSIGADVSHLNLHKTFAIPHGGGGPG 721

Query: 721 MGPIGVKAHLAPFVPGHSVVQIEGMLTRQGAVSAAPFGSASILPISWMYIRMMGAEGLKK 780
           MGPIGVKAHLAPFV GH+VV+        GAVSAAP+GSASILPI+WMYI+++G +GL++
Sbjct: 722 MGPIGVKAHLAPFVAGHAVVKHGRESDNNGAVSAAPYGSASILPITWMYIKLLGYQGLRQ 781

Query: 781 ASQVAILNANYIASRLQDAFPVLYTGRDGRVAHECILDIRPLKEETGISELDIAKRLIDY 840
           ++Q+A+LNANY+  +L   +PVLYTGR+ RVAHECI+D+RPLKE +G++E+DIAKRL DY
Sbjct: 782 STQMALLNANYVMKKLSAHYPVLYTGRNDRVAHECIIDLRPLKEASGVTEMDIAKRLNDY 841

Query: 841 GFHAPTMSFPVAGTLMVEPTESESKVELDRFIDAMLAIRAEIDQVKAGVWPLEDNPLVNA 900
           GFHAPTMSFPVAGTLM+EPTESESK ELDRFI+AM+AIR EI +V+AG WP ++NPL NA
Sbjct: 842 GFHAPTMSFPVAGTLMIEPTESESKAELDRFIEAMVAIRGEIAKVEAGEWPADNNPLHNA 901

Query: 901 PHIQSELV-AEW-AHPYSREVAVFPAGV--ADKYWPTVKRLDDVYGDRNLFCSCVPISEY 956
           PH  ++++ +E+ + PYSRE AVFP     A+K+WPTV R+DDVYGDRNL CSC PI +Y
Sbjct: 902 PHTMADIMDSEFDSRPYSRETAVFPTAAVKANKFWPTVNRIDDVYGDRNLMCSCAPIDDY 961

Query: 957 Q 957
           +
Sbjct: 962 K 962


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: 2256
Number of extensions: 82
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: 962
Length adjustment: 44
Effective length of query: 913
Effective length of database: 918
Effective search space:   838134
Effective search space used:   838134
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 5210634 Shew_3062 (glycine dehydrogenase (RefSeq))
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.2907.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 1534.3   0.6          0 1534.1   0.6    1.0  1  lcl|FitnessBrowser__PV4:5210634  Shew_3062 glycine dehydrogenase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5210634  Shew_3062 glycine dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1534.1   0.6         0         0       1     939 []      18     955 ..      18     955 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1534.1 bits;  conditional E-value: 0
                        TIGR00461   1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvksyiGkGyyatil 78 
                                      rh+Gpd+a+q++ml+ +G+++l++l++q+vp++irl r l ++++  e e la ++k a+knk++ksyiG+Gyy+ti+
  lcl|FitnessBrowser__PV4:5210634  18 RHIGPDSADQQEMLNFVGAESLEDLTQQIVPESIRLGRDLAVGSACGEAEGLASIRKYADKNKVFKSYIGMGYYGTIV 95 
                                      9***************************************************************************** PP

                        TIGR00461  79 ppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegtaaaeamalsfrvskkk.ank 155
                                      p viqrn++enpgwytaytpyqpei+qGrlea+lnfq++ +dltGl++a+asllde+taaaeamal++rvsk k an 
  lcl|FitnessBrowser__PV4:5210634  96 PSVIQRNVFENPGWYTAYTPYQPEIAQGRLEAILNFQQLSMDLTGLDLASASLLDEATAAAEAMALAKRVSKAKkANI 173
                                      ************************************************************************88799* PP

                        TIGR00461 156 fvvakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqypatdGeildykalidelksrkalvsvaadll 233
                                      f++a+dv pqt++vvktrae +g+e++v+ as+   + +++G+l qy+   G+i d+++l  +l+++ka+v+vaad++
  lcl|FitnessBrowser__PV4:5210634 174 FFIADDVFPQTIDVVKTRAECFGFEIVVGPASEAV-NYELFGALFQYTNHYGQITDFTELFAALQEKKAVVTVAADIM 250
                                      ******************************99975.579*************************************** PP

                        TIGR00461 234 altlltppgklGadivlGsaqrfGvplGyGGphaaffavkdeykrklpGrivGvskdalGntalrlalqtreqhirrd 311
                                      +l+ l++pg +Gad+v+GsaqrfGvp+G+GGphaaff ++d++kr+lpGri+Gvs+d+ Gn alr+a+qtreqhirr+
  lcl|FitnessBrowser__PV4:5210634 251 SLVSLKSPGSMGADVVFGSAQRFGVPMGFGGPHAAFFVTRDQHKRSLPGRIIGVSQDTRGNRALRMAMQTREQHIRRE 328
                                      ****************************************************************************** PP

                        TIGR00461 312 katsnictaqvllanvaslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtltvevgekaasevlka 389
                                      ka+snictaqvllan+as yav+hGp+Glk ia ri+rl++i+aaglk k+ el n+t+fdt++ +v++ aa   + +
  lcl|FitnessBrowser__PV4:5210634 329 KANSNICTAQVLLANMASFYAVFHGPQGLKIIADRIHRLADIFAAGLKAKGVELVNNTWFDTVSFKVADSAA--AQAR 404
                                      *********************************************************************999..6788 PP

                        TIGR00461 390 aeeaeinlravvltevgialdetttkedvldllkvlagkdnlglsseelsedvan....sfpaellrddeilrdevfn 463
                                      a + e+nlr +  + +g+a+ ettt+edv +l+++++g+  +gl++  ++ d+      s+pael r+d il+++ fn
  lcl|FitnessBrowser__PV4:5210634 405 AIAGEVNLRIDSDGILGVAMAETTTREDVAQLFDIVLGE-GHGLDVAAIDADIIAngsnSIPAELVRQDAILEHPTFN 481
                                      8899**********************************5.5*******99998444555******************* PP

                        TIGR00461 464 ryhsetellrylhrleskdlalnqsmiplGsctmklnataemlpitwpefaeihpfapaeqveGykeliaqlekwlve 541
                                      ryhsete++ry++rle+kdlaln+smi lGsctmklna++em+p++wpef+++hpf+p +q++Gy eli +l +wlv+
  lcl|FitnessBrowser__PV4:5210634 482 RYHSETEMMRYIKRLENKDLALNHSMISLGSCTMKLNAATEMMPVSWPEFGNMHPFCPQDQAQGYAELIEELSNWLVD 559
                                      ****************************************************************************** PP

                        TIGR00461 542 itGfdaislqpnsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpasaamaGlkvvpvkcdkeGnidlvdlk 619
                                      itG+da+++qpnsGa GeyaGl +i++yhesrge+hrn+clip+sahGtnpasa++aG+k+v+ +cdk+Gn+d++dlk
  lcl|FitnessBrowser__PV4:5210634 560 ITGYDAMCMQPNSGASGEYAGLLAIKKYHESRGEGHRNVCLIPQSAHGTNPASAQLAGMKIVVTACDKQGNVDMEDLK 637
                                      ****************************************************************************** PP

                        TIGR00461 620 akaekagdelaavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGltspgdlGadvchlnlhktfsiph 697
                                      aka + +++l+++mvtypst+Gv+eeti e+++++h+ GGqvyldGanmnaqvGltspg +Gadv+hlnlhktf+iph
  lcl|FitnessBrowser__PV4:5210634 638 AKAAEVAENLSCIMVTYPSTHGVYEETISEICEVIHQHGGQVYLDGANMNAQVGLTSPGSIGADVSHLNLHKTFAIPH 715
                                      ****************************************************************************** PP

                        TIGR00461 698 GGGGpgmgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasilpisymyikmmGaeGlkkasevailna 775
                                      GGGGpgmgpigvk+hlapf+ +   + vv+   es + gavsaapyGsasilpi++myik++G +Gl++++++a+lna
  lcl|FitnessBrowser__PV4:5210634 716 GGGGPGMGPIGVKAHLAPFVAG---HAVVKHGRESDNNGAVSAAPYGSASILPITWMYIKLLGYQGLRQSTQMALLNA 790
                                      **********************...7788999999******************************************* PP

                        TIGR00461 776 nylakrlkdaykilfvgrdervahecildlrelkekagiealdvakrlldyGfhaptlsfpvaGtlmvepteseslee 853
                                      ny++k+l  +y++l++gr++rvaheci+dlr+lke +g+ ++d+akrl dyGfhapt+sfpvaGtlm+epteses+ e
  lcl|FitnessBrowser__PV4:5210634 791 NYVMKKLSAHYPVLYTGRNDRVAHECIIDLRPLKEASGVTEMDIAKRLNDYGFHAPTMSFPVAGTLMIEPTESESKAE 868
                                      ****************************************************************************** PP

                        TIGR00461 854 ldrfidamiaikeeidavkaGeiklednilknaphslqslivaewad.pysreeaaypapvlkyfkfwptvarlddty 930
                                      ldrfi+am+ai+ ei +v aGe+++++n+l+naph++ + + +e+   pysre a++p + +k +kfwptv+r+dd+y
  lcl|FitnessBrowser__PV4:5210634 869 LDRFIEAMVAIRGEIAKVEAGEWPADNNPLHNAPHTMADIMDSEFDSrPYSRETAVFPTAAVKANKFWPTVNRIDDVY 946
                                      ********************************************96526***************************** PP

                        TIGR00461 931 Gdrnlvcsc 939
                                      Gdrnl+csc
  lcl|FitnessBrowser__PV4:5210634 947 GDRNLMCSC 955
                                      ********* PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (939 nodes)
Target sequences:                          1  (962 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: 00:00:00.07
# Mc/sec: 12.05
//
[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