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

GapMind for catabolism of small carbon sources

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

Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate AO353_07560 AO353_07560 malate synthase G

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



>FitnessBrowser__pseudo3_N2E3:AO353_07560
          Length = 725

 Score = 1221 bits (3159), Expect = 0.0
 Identities = 591/726 (81%), Positives = 666/726 (91%), Gaps = 1/726 (0%)

Query: 1   MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60
           MTE VQVGGLQVAKVL+DFVNNEAIPG+G+ A  FWAGAD VIHDLAPKN+ALLAKRDDL
Sbjct: 1   MTEHVQVGGLQVAKVLFDFVNNEAIPGSGLTADKFWAGADKVIHDLAPKNKALLAKRDDL 60

Query: 61  QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120
           QA+IDAWHQ+RAGQAHDAVAYK+FLQ+IGYLLPEA DFQATT+NVD+EIARMAGPQLVVP
Sbjct: 61  QARIDAWHQSRAGQAHDAVAYKAFLQDIGYLLPEAADFQATTQNVDDEIARMAGPQLVVP 120

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

Query: 181 PLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHF 240
           PL  GSHVDSTGY+I   KLVVSLK GS +GL+N AQL GF G+A+AP A+LLKNNG+HF
Sbjct: 181 PLAAGSHVDSTGYKIVDRKLVVSLKGGSNSGLRNDAQLIGFHGDAAAPTAILLKNNGLHF 240

Query: 241 EIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDL 300
           EIQID ++P+GQTDAAGVKD+LME+ALTTIMDCEDS+AAVDADDK V+YRNWLGLMKGDL
Sbjct: 241 EIQIDASTPVGQTDAAGVKDVLMEAALTTIMDCEDSVAAVDADDKVVIYRNWLGLMKGDL 300

Query: 301 VEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEV 360
            EE+ KGGK  TR MN DR YT  DG+ EL+LHGRSLLF+RNVGHLMT DAILDK GNEV
Sbjct: 301 SEEVAKGGKTFTRTMNADRTYTAPDGS-ELSLHGRSLLFVRNVGHLMTIDAILDKNGNEV 359

Query: 361 PEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLG 420
           PEGI+DGL T+L A+H+LNGNT+RKN+RTGS+YIVKPKMHGPEE AF  ELFGR+EDVL 
Sbjct: 360 PEGILDGLVTNLAALHSLNGNTTRKNSRTGSVYIVKPKMHGPEEAAFTNELFGRIEDVLE 419

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

Query: 481 AMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTAW 540
            MKAEKWISAYEN NVD+GL+ GLQG+AQIGKGMWAMPDLMAAMLEQK+ HP+AGANTAW
Sbjct: 480 DMKAEKWISAYENWNVDIGLSTGLQGRAQIGKGMWAMPDLMAAMLEQKIAHPLAGANTAW 539

Query: 541 VPSPTAATLHAMHYHKIDVQARQVELAKREKASIDDILTIPLAQDTNWSEEEKRNELDNN 600
           VPSPTAA LHA+HYHK+DV ARQ ELAKR +AS+DDILTIPLA D NW+ E+ +NELDNN
Sbjct: 540 VPSPTAAALHALHYHKVDVFARQAELAKRARASLDDILTIPLASDPNWTAEQIQNELDNN 599

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

Query: 661 LKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHRRRREF 720
           LKRMAPVVDRQN  DPLYRP+AP+FD+++AFQAA+ELV+EGTKQPNGYTEPVLHRRRREF
Sbjct: 660 LKRMAPVVDRQNANDPLYRPLAPNFDSNIAFQAAVELVIEGTKQPNGYTEPVLHRRRREF 719

Query: 721 KAKNGL 726
           KA NGL
Sbjct: 720 KAANGL 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: 1627
Number of extensions: 51
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 AO353_07560 AO353_07560 (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.11882.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 1217.2   1.6          0 1217.0   1.6    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_07560  AO353_07560 malate synthase G


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_07560  AO353_07560 malate synthase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1217.0   1.6         0         0       2     720 ..       4     722 ..       3     723 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1217.0 bits;  conditional E-value: 0
                                     TIGR01345   2 rvdagrlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaideyh 66 
                                                   +v++g+lqvak+l dfv++e++pg g+ a+kfw+g d++++dlap+n+ llakrd++qa id++h
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_07560   4 HVQVGGLQVAKVLFDFVNNEAIPGSGLTADKFWAGADKVIHDLAPKNKALLAKRDDLQARIDAWH 68 
                                                   6899************************************************************* PP

                                     TIGR01345  67 rknk.gvidkeayksflkeigylveepervtietenvdseiasqagpqlvvpvlnaryalnaana 130
                                                   ++    + d  ayk fl++igyl +e    + +t+nvd+eia  agpqlvvpv+nar+alna+na
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_07560  69 QSRAgQAHDAVAYKAFLQDIGYLLPEAADFQATTQNVDDEIARMAGPQLVVPVMNARFALNASNA 133
                                                   **99557899******************************************************* PP

                                     TIGR01345 131 rwgslydalygsnvipeedgaekgkeynpkrgekviefarefldeslplesgsyadvvkykivdk 195
                                                   rwgslydalyg+++i+e dgaekgk yn +rg+kvi+far flde+ pl +gs+ d   ykivd+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_07560 134 RWGSLYDALYGTDAISEADGAEKGKGYNKVRGDKVIAFARAFLDEAAPLAAGSHVDSTGYKIVDR 198
                                                   ***************************************************************** PP

                                     TIGR01345 196 klavqlesgkvtrlkdeeqfvgyrgdaadpevillktnglhielqidarhpigkadkakvkdivl 260
                                                   kl+v l+ g+   l++++q +g++gdaa+p++illk+nglh e+qida  p+g++d a+vkd+++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_07560 199 KLVVSLKGGSNSGLRNDAQLIGFHGDAAAPTAILLKNNGLHFEIQIDASTPVGQTDAAGVKDVLM 263
                                                   ***************************************************************** PP

                                     TIGR01345 261 esaittildcedsvaavdaedkvlvyrnllglmkgtlkeklekngriikrklnedrsytaangee 325
                                                   e+a+tti+dcedsvaavda+dkv++yrn+lglmkg+l e++ k g++++r +n dr+yta++g+e
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_07560 264 EAALTTIMDCEDSVAAVDADDKVVIYRNWLGLMKGDLSEEVAKGGKTFTRTMNADRTYTAPDGSE 328
                                                   ***************************************************************** PP

                                     TIGR01345 326 lslhgrsllfvrnvghlmtipviltdegeeipegildgvltsvialydlkvqnklrnsrkgsvyi 390
                                                   lslhgrsllfvrnvghlmti +il+++g+e+pegildg++t++ al+ l+ + + +nsr+gsvyi
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_07560 329 LSLHGRSLLFVRNVGHLMTIDAILDKNGNEVPEGILDGLVTNLAALHSLNGNTTRKNSRTGSVYI 393
                                                   ***************************************************************** PP

                                     TIGR01345 391 vkpkmhgpeevafanklftriedllglerhtlkvgvmdeerrtslnlkaciakvkervafintgf 455
                                                   vkpkmhgpee af+n+lf+ried+l+l+r+tlkvg+mdeerrt++nlkaci+ + erv+fintgf
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_07560 394 VKPKMHGPEEAAFTNELFGRIEDVLELPRNTLKVGIMDEERRTTVNLKACIKAASERVVFINTGF 458
                                                   ***************************************************************** PP

                                     TIGR01345 456 ldrtgdeihtsmeagamvrkadmksapwlkayernnvaagltcglrgkaqigkgmwampdlmaem 520
                                                   ldrtgdeihtsmeagamvrkadmk+  w++aye+ nv+ gl +gl+g+aqigkgmwampdlma m
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_07560 459 LDRTGDEIHTSMEAGAMVRKADMKAEKWISAYENWNVDIGLSTGLQGRAQIGKGMWAMPDLMAAM 523
                                                   ***************************************************************** PP

                                     TIGR01345 521 lekkgdqlragantawvpsptaatlhalhyhrvdvqkvqkeladaerraelkeiltipvaentnw 585
                                                   le+k+  + agantawvpsptaa+lhalhyh+vdv++ q+ela+   ra+l++iltip+a++ nw
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_07560 524 LEQKIAHPLAGANTAWVPSPTAAALHALHYHKVDVFARQAELAKR-ARASLDDILTIPLASDPNW 587
                                                   *******************************************99.899**************** PP

                                     TIGR01345 586 seeeikeeldnnvqgilgyvvrwveqgigcskvpdihnvalmedratlrissqhlanwlrhgivs 650
                                                   ++e+i++eldnn+qgilgyvvrw++qg+gcskvpdi +v lmedratlrissqh+anwlrhgivs
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_07560 588 TAEQIQNELDNNAQGILGYVVRWIDQGVGCSKVPDINDVGLMEDRATLRISSQHIANWLRHGIVS 652
                                                   ***************************************************************** PP

                                     TIGR01345 651 keqvleslermakvvdkqnagdeayrpmadnleasvafkaakdlilkgtkqpsgytepilharrl 715
                                                     qvle+l+rma vvd+qna d+ yrp+a+n+++ +af+aa +l+++gtkqp+gytep+lh+rr+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_07560 653 EAQVLETLKRMAPVVDRQNANDPLYRPLAPNFDSNIAFQAAVELVIEGTKQPNGYTEPVLHRRRR 717
                                                   ***************************************************************** PP

                                     TIGR01345 716 efkek 720
                                                   efk+ 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_07560 718 EFKAA 722
                                                   ***86 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.04
# Mc/sec: 10.77
//
[ok]

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

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Protein sequences (fasta format)
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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