Alignments for a candidate for glcB in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Alignments for a candidate for glcB in Desulfovibrio vulgaris Hildenborough

Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate 206126 DVU0701 malate synthase G

Query= reanno::psRCH2:GFF353
         (726 letters)



>MicrobesOnline__882:206126
          Length = 729

 Score =  873 bits (2255), Expect = 0.0
 Identities = 421/728 (57%), Positives = 538/728 (73%), Gaps = 6/728 (0%)

Query: 1   MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60
           MT R++ GGL VA+ L+  +  E +PGTG+  + FWAG + ++  L P+NR LLA+RD++
Sbjct: 1   MTGRIREGGLAVAEPLHRCIEREILPGTGISPSIFWAGLEELVGTLGPRNRELLARRDNM 60

Query: 61  QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120
           QA IDAWH+   G+ HDA AY+ FL++I YLLP  +D    T+ VD E+A +AGPQLVVP
Sbjct: 61  QAAIDAWHKEHQGRPHDAAAYRRFLEDIRYLLPAPQDLAVETQGVDPEVATIAGPQLVVP 120

Query: 121 IMNARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAA 180
           + N R+ALNA NARWGSLYDALYG+D I+++DGA++G  YN +RG KV+AYA  FL+   
Sbjct: 121 VTNPRYALNAVNARWGSLYDALYGSDVIADSDGAARGAAYNPLRGAKVVAYAAAFLDRTF 180

Query: 181 PLETGSHVDSTGYRIEGG----KLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNN 236
           PL    H D   Y + G     KL     DG+ TGL +P    G+ G    P  VLL+NN
Sbjct: 181 PLAGARHADVVRYELTGPPVGRKLSALCADGTVTGLLHPDAFAGYTG-GERPTTVLLRNN 239

Query: 237 GIHFEIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLM 296
           G+H E+Q D   P+G    AG+KD+++ESA+TTI+DCEDS+A VDA+DK + YRN LGL 
Sbjct: 240 GLHVELQFDRRHPVGAAHPAGLKDVVLESAVTTILDCEDSVATVDAEDKALAYRNLLGLF 299

Query: 297 KGDLVEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKE 356
           +GDL    +KGG+ + R +  DR YT A G     L GRSL+ +RNVG LMT DA+LD  
Sbjct: 300 RGDLETSFDKGGRSVFRRLAADRTYT-APGGAAYALPGRSLMLVRNVGLLMTTDAVLDAA 358

Query: 357 GNEVPEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVE 416
           G E+PEGI+DGL T+ I +H+L G    +N+  GS+YIVKPK+HGPEEVAF  E F R+E
Sbjct: 359 GQEIPEGILDGLVTACIGLHDLRGAGRHRNSGAGSVYIVKPKLHGPEEVAFVCEQFRRIE 418

Query: 417 DVLGLPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPM 476
           D+LG+ RNTLK+G+MDEERRTT+NL  CI+ A +R++FINTGFLDRTGDEIHT MEAGP+
Sbjct: 419 DILGMARNTLKMGVMDEERRTTLNLAECIRVASQRIIFINTGFLDRTGDEIHTCMEAGPV 478

Query: 477 VRKAAMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGA 536
           VRK  MKA++W+ AYE+ NVD GLA G  GKAQIGKGMW  PD +A M+  K  HP AGA
Sbjct: 479 VRKNDMKAQRWMLAYEDWNVDTGLAAGFGGKAQIGKGMWPKPDRLAEMVATKGAHPRAGA 538

Query: 537 NTAWVPSPTAATLHAMHYHKIDVQARQVELAKREKASIDDILTIPLAQDTNWSEEEKRNE 596
           N AWVPSPTAATLHA+HYH++DV ARQ ELA   +AS+DD+L +PL  +   S  E R E
Sbjct: 539 NCAWVPSPTAATLHALHYHEVDVFARQRELAGCHRASLDDLLALPLMGEARPSPAEVREE 598

Query: 597 LDNNSQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKDQ 656
           L+NN+Q ILGY+VRWVE G+GCSKVPDI+D+ LMEDRATLRISSQH+ANW+RHG+ T+D+
Sbjct: 599 LENNAQSILGYVVRWVEMGIGCSKVPDIHDVGLMEDRATLRISSQHIANWLRHGICTEDE 658

Query: 657 VVESLKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHRR 716
           V + + RMA VVDRQN+ +P YRPM+ D  +SVAF+AA +LV EG +QPNGYTEP+LH R
Sbjct: 659 VRDVMLRMATVVDRQNKDEPGYRPMSADPGSSVAFRAACDLVFEGARQPNGYTEPILHAR 718

Query: 717 RREFKAKN 724
           RRE KA++
Sbjct: 719 RREVKARS 726


Lambda     K      H
   0.316    0.133    0.386 

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: 1384
Number of extensions: 55
Number of successful extensions: 5
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: 726
Length of database: 729
Length adjustment: 40
Effective length of query: 686
Effective length of database: 689
Effective search space:   472654
Effective search space used:   472654
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)

Align candidate 206126 DVU0701 (malate synthase G)
to HMM TIGR01345 (glcB: malate synthase G (EC 2.3.3.9))

# 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/TIGR01345.hmm
# target sequence database:        /tmp/gapView.30164.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01345  [M=721]
Accession:   TIGR01345
Description: malate_syn_G: malate synthase G
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 1048.0   0.0          0 1047.8   0.0    1.0  1  lcl|MicrobesOnline__882:206126  DVU0701 malate synthase G


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:206126  DVU0701 malate synthase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1047.8   0.0         0         0       3     720 ..       5     725 ..       3     726 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1047.8 bits;  conditional E-value: 0
                       TIGR01345   3 vdagrlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaideyhrknk.gvidkeayks 80 
                                     +  g+l va+ l++ +e+e+lpgtg+    fw+g++e+v  l p+nrella+rd++qaaid++h++ +  + d +ay+ 
  lcl|MicrobesOnline__882:206126   5 IREGGLAVAEPLHRCIEREILPGTGISPSIFWAGLEELVGTLGPRNRELLARRDNMQAAIDAWHKEHQgRPHDAAAYRR 83 
                                     67899*************************************************************995689******* PP

                       TIGR01345  81 flkeigylveepervtietenvdseiasqagpqlvvpvlnaryalnaanarwgslydalygsnvipeedgaekgkeynp 159
                                     fl++i yl + p+   +et++vd e+a+ agpqlvvpv+n ryalna narwgslydalygs+vi++ dga +g  ynp
  lcl|MicrobesOnline__882:206126  84 FLEDIRYLLPAPQDLAVETQGVDPEVATIAGPQLVVPVTNPRYALNAVNARWGSLYDALYGSDVIADSDGAARGAAYNP 162
                                     ******************************************************************************* PP

                       TIGR01345 160 krgekviefarefldeslplesgsyadvvkyki....vdkklavqlesgkvtrlkdeeqfvgyrgdaadpevillktng 234
                                      rg kv+++a  fld+++pl ++ +advv+y++    v +kl +   +g vt l +++ f gy+g    p+++ll++ng
  lcl|MicrobesOnline__882:206126 163 LRGAKVVAYAAAFLDRTFPLAGARHADVVRYELtgppVGRKLSALCADGTVTGLLHPDAFAGYTGGE-RPTTVLLRNNG 240
                                     ********************************93333468999999*******************86.7********** PP

                       TIGR01345 235 lhielqidarhpigkadkakvkdivlesaittildcedsvaavdaedkvlvyrnllglmkgtlkeklekngriikrkln 313
                                     lh+elq d rhp+g a +a++kd+vlesa+ttildcedsva+vdaedk l yrnllgl +g+l+  ++k gr + r+l 
  lcl|MicrobesOnline__882:206126 241 LHVELQFDRRHPVGAAHPAGLKDVVLESAVTTILDCEDSVATVDAEDKALAYRNLLGLFRGDLETSFDKGGRSVFRRLA 319
                                     ******************************************************************************* PP

                       TIGR01345 314 edrsytaangeelslhgrsllfvrnvghlmtipviltdegeeipegildgvltsvialydlkvqnklrnsrkgsvyivk 392
                                      dr+yta+ g   +l+grsl++vrnvg lmt+ ++l+  g+eipegildg++t+ i l+dl+  ++ rns  gsvyivk
  lcl|MicrobesOnline__882:206126 320 ADRTYTAPGGAAYALPGRSLMLVRNVGLLMTTDAVLDAAGQEIPEGILDGLVTACIGLHDLRGAGRHRNSGAGSVYIVK 398
                                     ******************************************************************************* PP

                       TIGR01345 393 pkmhgpeevafanklftriedllglerhtlkvgvmdeerrtslnlkaciakvkervafintgfldrtgdeihtsmeaga 471
                                     pk+hgpeevaf  + f ried+lg++r+tlk+gvmdeerrt+lnl  ci  + +r++fintgfldrtgdeiht+meag+
  lcl|MicrobesOnline__882:206126 399 PKLHGPEEVAFVCEQFRRIEDILGMARNTLKMGVMDEERRTTLNLAECIRVASQRIIFINTGFLDRTGDEIHTCMEAGP 477
                                     ******************************************************************************* PP

                       TIGR01345 472 mvrkadmksapwlkayernnvaagltcglrgkaqigkgmwampdlmaemlekkgdqlragantawvpsptaatlhalhy 550
                                     +vrk+dmk+  w+ aye  nv++gl +g+ gkaqigkgmw  pd +aem+  kg  +ragan awvpsptaatlhalhy
  lcl|MicrobesOnline__882:206126 478 VVRKNDMKAQRWMLAYEDWNVDTGLAAGFGGKAQIGKGMWPKPDRLAEMVATKGAHPRAGANCAWVPSPTAATLHALHY 556
                                     ******************************************************************************* PP

                       TIGR01345 551 hrvdvqkvqkeladaerraelkeiltipvaentnwseeeikeeldnnvqgilgyvvrwveqgigcskvpdihnvalmed 629
                                     h+vdv++ q ela   +ra+l+++l +p+ +++  s  e++eel+nn+q+ilgyvvrwve gigcskvpdih+v lmed
  lcl|MicrobesOnline__882:206126 557 HEVDVFARQRELAGC-HRASLDDLLALPLMGEARPSPAEVREELENNAQSILGYVVRWVEMGIGCSKVPDIHDVGLMED 634
                                     *************99.999************************************************************ PP

                       TIGR01345 630 ratlrissqhlanwlrhgivskeqvleslermakvvdkqnagdeayrpmadnleasvafkaakdlilkgtkqpsgytep 708
                                     ratlrissqh+anwlrhgi + ++v + + rma vvd+qn  ++ yrpm+ +  +svaf+aa dl+++g++qp+gytep
  lcl|MicrobesOnline__882:206126 635 RATLRISSQHIANWLRHGICTEDEVRDVMLRMATVVDRQNKDEPGYRPMSADPGSSVAFRAACDLVFEGARQPNGYTEP 713
                                     ******************************************************************************* PP

                       TIGR01345 709 ilharrlefkek 720
                                     ilharr+e k++
  lcl|MicrobesOnline__882:206126 714 ILHARRREVKAR 725
                                     *********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (721 nodes)
Target sequences:                          1  (729 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 9.37
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources