Alignments for a candidate for glcB in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for glcB in Pseudomonas simiae WCS417

Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate GFF5083 PS417_26040 malate synthase

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



>FitnessBrowser__WCS417:GFF5083
          Length = 725

 Score = 1229 bits (3180), Expect = 0.0
 Identities = 592/726 (81%), Positives = 666/726 (91%), Gaps = 1/726 (0%)

Query: 1   MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60
           MTE VQVGGLQVAKVL+DFVNNEAIPGTG+ A  FWAGAD VIHDLAPKN+ALLAKRDD 
Sbjct: 1   MTEHVQVGGLQVAKVLFDFVNNEAIPGTGITADQFWAGADKVIHDLAPKNKALLAKRDDF 60

Query: 61  QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120
           QA+ID WHQ  AGQAHD VAYK+FLQ+IGYLLPEA DFQATT+NVD+EIARMAGPQLVVP
Sbjct: 61  QARIDTWHQTHAGQAHDPVAYKAFLQDIGYLLPEAADFQATTQNVDDEIARMAGPQLVVP 120

Query: 121 IMNARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAA 180
           +MNARFALNA+NARWGSLYDALYGTDAISEADGA KG GYN++RG+KVIA+AR FL+EAA
Sbjct: 121 VMNARFALNASNARWGSLYDALYGTDAISEADGAEKGQGYNKVRGDKVIAFARAFLDEAA 180

Query: 181 PLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHF 240
           PL  GSHVDSTGY+I  GKL+VSLK GS +GL++ AQL GFQG A+ PIA+LLK+NG+HF
Sbjct: 181 PLSAGSHVDSTGYKIVDGKLIVSLKGGSNSGLRDDAQLIGFQGPAAQPIAILLKHNGLHF 240

Query: 241 EIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDL 300
           EIQID ++P+GQTDAAG+KD+LME+ALTTIMDCEDS+AAVDADDK V+YRNWLGLMKGDL
Sbjct: 241 EIQIDASTPVGQTDAAGIKDVLMEAALTTIMDCEDSVAAVDADDKVVIYRNWLGLMKGDL 300

Query: 301 VEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEV 360
            EE+ KGGK  TR MN DRVYT  +G  ++TLHGRSLLF+RNVGHLMT DAILDK+GNEV
Sbjct: 301 AEEVAKGGKTFTRTMNADRVYTGVNGQ-DVTLHGRSLLFVRNVGHLMTIDAILDKDGNEV 359

Query: 361 PEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLG 420
           PEGI+DGL TSL A+H+LNGN+SRKN+RTGS+YIVKPKMHGPEE AF  ELFGR+E+VL 
Sbjct: 360 PEGILDGLITSLAAIHSLNGNSSRKNSRTGSVYIVKPKMHGPEEAAFTNELFGRIENVLN 419

Query: 421 LPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVRKA 480
           LPRNTLKVGIMDEERRTT+NLKACIK A ERVVFINTGFLDRTGDEIHTSMEAG MVRKA
Sbjct: 420 LPRNTLKVGIMDEERRTTVNLKACIKAASERVVFINTGFLDRTGDEIHTSMEAGAMVRKA 479

Query: 481 AMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTAW 540
           AMKAEKWISAYEN NVD+GL+ GLQG+AQIGKGMWAMPDLMAAMLEQK+ HP+AGANTAW
Sbjct: 480 AMKAEKWISAYENWNVDIGLSTGLQGRAQIGKGMWAMPDLMAAMLEQKIAHPLAGANTAW 539

Query: 541 VPSPTAATLHAMHYHKIDVQARQVELAKREKASIDDILTIPLAQDTNWSEEEKRNELDNN 600
           VPSPTAA LH +HYHK+DV ARQ ELAKRE+AS+DDILTIPLA +TNWS+EE RNELDNN
Sbjct: 540 VPSPTAAALHVLHYHKVDVFARQAELAKRERASVDDILTIPLASNTNWSDEEIRNELDNN 599

Query: 601 SQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKDQVVES 660
           +QGILGY+VRW++QGVGCSKVPDIND+ LMEDRATLRISSQH+ANW+RHG+V + QV+ES
Sbjct: 600 AQGILGYVVRWIDQGVGCSKVPDINDVGLMEDRATLRISSQHIANWLRHGIVNEVQVMES 659

Query: 661 LKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHRRRREF 720
           LKRMAPVVDRQN GD LYRP+APDFD+++AFQAA+ELV+EGTKQPNGYTEPVLHRRRREF
Sbjct: 660 LKRMAPVVDRQNAGDKLYRPLAPDFDSNIAFQAAVELVIEGTKQPNGYTEPVLHRRRREF 719

Query: 721 KAKNGL 726
           KAKNGL
Sbjct: 720 KAKNGL 725


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: 1640
Number of extensions: 49
Number of successful extensions: 2
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: 725
Length adjustment: 40
Effective length of query: 686
Effective length of database: 685
Effective search space:   469910
Effective search space used:   469910
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 GFF5083 PS417_26040 (malate synthase)
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.7489.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 1202.9   2.6          0 1202.7   2.6    1.0  1  lcl|FitnessBrowser__WCS417:GFF5083  PS417_26040 malate synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF5083  PS417_26040 malate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1202.7   2.6         0         0       2     721 .]       4     723 ..       3     723 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1202.7 bits;  conditional E-value: 0
                           TIGR01345   2 rvdagrlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaideyhrknk.gvidk 75 
                                         +v++g+lqvak+l dfv++e++pgtg+ a++fw+g d++++dlap+n+ llakrd++qa id +h+     + d 
  lcl|FitnessBrowser__WCS417:GFF5083   4 HVQVGGLQVAKVLFDFVNNEAIPGTGITADQFWAGADKVIHDLAPKNKALLAKRDDFQARIDTWHQTHAgQAHDP 78 
                                         6899***************************************************************99557899 PP

                           TIGR01345  76 eayksflkeigylveepervtietenvdseiasqagpqlvvpvlnaryalnaanarwgslydalygsnvipeedg 150
                                          ayk fl++igyl +e    + +t+nvd+eia  agpqlvvpv+nar+alna+narwgslydalyg+++i+e dg
  lcl|FitnessBrowser__WCS417:GFF5083  79 VAYKAFLQDIGYLLPEAADFQATTQNVDDEIARMAGPQLVVPVMNARFALNASNARWGSLYDALYGTDAISEADG 153
                                         *************************************************************************** PP

                           TIGR01345 151 aekgkeynpkrgekviefarefldeslplesgsyadvvkykivdkklavqlesgkvtrlkdeeqfvgyrgdaadp 225
                                         aekg+ yn +rg+kvi+far flde+ pl++gs+ d   ykivd+kl v l+ g+   l+d++q +g++g aa+p
  lcl|FitnessBrowser__WCS417:GFF5083 154 AEKGQGYNKVRGDKVIAFARAFLDEAAPLSAGSHVDSTGYKIVDGKLIVSLKGGSNSGLRDDAQLIGFQGPAAQP 228
                                         *************************************************************************** PP

                           TIGR01345 226 evillktnglhielqidarhpigkadkakvkdivlesaittildcedsvaavdaedkvlvyrnllglmkgtlkek 300
                                          +illk+nglh e+qida  p+g++d a++kd+++e+a+tti+dcedsvaavda+dkv++yrn+lglmkg+l e+
  lcl|FitnessBrowser__WCS417:GFF5083 229 IAILLKHNGLHFEIQIDASTPVGQTDAAGIKDVLMEAALTTIMDCEDSVAAVDADDKVVIYRNWLGLMKGDLAEE 303
                                         *************************************************************************** PP

                           TIGR01345 301 lekngriikrklnedrsytaangeelslhgrsllfvrnvghlmtipviltdegeeipegildgvltsvialydlk 375
                                         + k g++++r +n dr+yt+ ng++++lhgrsllfvrnvghlmti +il+++g+e+pegildg++ts+ a++ l+
  lcl|FitnessBrowser__WCS417:GFF5083 304 VAKGGKTFTRTMNADRVYTGVNGQDVTLHGRSLLFVRNVGHLMTIDAILDKDGNEVPEGILDGLITSLAAIHSLN 378
                                         *************************************************************************** PP

                           TIGR01345 376 vqnklrnsrkgsvyivkpkmhgpeevafanklftriedllglerhtlkvgvmdeerrtslnlkaciakvkervaf 450
                                          +++ +nsr+gsvyivkpkmhgpee af+n+lf+rie++l+l+r+tlkvg+mdeerrt++nlkaci+ + erv+f
  lcl|FitnessBrowser__WCS417:GFF5083 379 GNSSRKNSRTGSVYIVKPKMHGPEEAAFTNELFGRIENVLNLPRNTLKVGIMDEERRTTVNLKACIKAASERVVF 453
                                         *************************************************************************** PP

                           TIGR01345 451 intgfldrtgdeihtsmeagamvrkadmksapwlkayernnvaagltcglrgkaqigkgmwampdlmaemlekkg 525
                                         intgfldrtgdeihtsmeagamvrka mk+  w++aye+ nv+ gl +gl+g+aqigkgmwampdlma mle+k+
  lcl|FitnessBrowser__WCS417:GFF5083 454 INTGFLDRTGDEIHTSMEAGAMVRKAAMKAEKWISAYENWNVDIGLSTGLQGRAQIGKGMWAMPDLMAAMLEQKI 528
                                         *************************************************************************** PP

                           TIGR01345 526 dqlragantawvpsptaatlhalhyhrvdvqkvqkeladaerraelkeiltipvaentnwseeeikeeldnnvqg 600
                                           + agantawvpsptaa+lh lhyh+vdv++ q+ela+  +ra+ ++iltip+a+ntnws+eei++eldnn+qg
  lcl|FitnessBrowser__WCS417:GFF5083 529 AHPLAGANTAWVPSPTAAALHVLHYHKVDVFARQAELAKR-ERASVDDILTIPLASNTNWSDEEIRNELDNNAQG 602
                                         **************************************99.7899****************************** PP

                           TIGR01345 601 ilgyvvrwveqgigcskvpdihnvalmedratlrissqhlanwlrhgivskeqvleslermakvvdkqnagdeay 675
                                         ilgyvvrw++qg+gcskvpdi +v lmedratlrissqh+anwlrhgiv   qv+esl+rma vvd+qnagd+ y
  lcl|FitnessBrowser__WCS417:GFF5083 603 ILGYVVRWIDQGVGCSKVPDINDVGLMEDRATLRISSQHIANWLRHGIVNEVQVMESLKRMAPVVDRQNAGDKLY 677
                                         *************************************************************************** PP

                           TIGR01345 676 rpmadnleasvafkaakdlilkgtkqpsgytepilharrlefkekn 721
                                         rp+a+++++ +af+aa +l+++gtkqp+gytep+lh+rr+efk+kn
  lcl|FitnessBrowser__WCS417:GFF5083 678 RPLAPDFDSNIAFQAAVELVIEGTKQPNGYTEPVLHRRRREFKAKN 723
                                         *******************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (721 nodes)
Target sequences:                          1  (725 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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 10.81
//
[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