Alignments for a candidate for glcB in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for glcB in Pseudomonas fluorescens FW300-N1B4

Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate Pf1N1B4_2478 Malate synthase G (EC 2.3.3.9)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2478
          Length = 725

 Score = 1228 bits (3178), Expect = 0.0
 Identities = 595/726 (81%), Positives = 667/726 (91%), Gaps = 1/726 (0%)

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

Query: 61  QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120
           QA+IDAWHQARAG AHDAVAYK+FLQ+IGYLLPEA DFQATT+NVD+EIARMAGPQLVVP
Sbjct: 61  QARIDAWHQARAGVAHDAVAYKAFLQDIGYLLPEAADFQATTQNVDDEIARMAGPQLVVP 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  GKLVV+LK GS TGL++ AQL GF G+ +AP A+LLKNNG+HF
Sbjct: 181 PLAAGSHVDSTGYKIIDGKLVVALKGGSNTGLRDDAQLIGFHGDTAAPTAILLKNNGLHF 240

Query: 241 EIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDL 300
           EIQID ++P+GQTDAAGVKDILME+ALTTIMDCEDS+AAVDADDK V+YRNWLGLMKGDL
Sbjct: 241 EIQIDASTPVGQTDAAGVKDILMEAALTTIMDCEDSVAAVDADDKVVIYRNWLGLMKGDL 300

Query: 301 VEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEV 360
            EE+ KGG+  TR MN DR YT  DG+ EL+LHGRSLLF+RNVGHLMT DAILDK+GNEV
Sbjct: 301 SEEVSKGGQTFTRTMNADRTYTALDGS-ELSLHGRSLLFVRNVGHLMTIDAILDKDGNEV 359

Query: 361 PEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLG 420
           PEGI+DGL T L A+H+LNGN+SRKN+RTGS+YIVKPKMHGPEE AF  ELFGR+EDVLG
Sbjct: 360 PEGILDGLVTCLAAIHSLNGNSSRKNSRTGSVYIVKPKMHGPEEAAFTNELFGRIEDVLG 419

Query: 421 LPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVRKA 480
           LPRNTLKVGIMDEERRTT+NLKACIK A ERVVFINTGFLDRTGDEIHTSMEAGPMVRKA
Sbjct: 420 LPRNTLKVGIMDEERRTTVNLKACIKAAAERVVFINTGFLDRTGDEIHTSMEAGPMVRKA 479

Query: 481 AMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTAW 540
            MKAEKWISAYEN NVD+GL+ GLQG+AQIGKGMWAMPDLMAAMLEQK+ HPMAGANTAW
Sbjct: 480 DMKAEKWISAYENWNVDIGLSTGLQGRAQIGKGMWAMPDLMAAMLEQKIAHPMAGANTAW 539

Query: 541 VPSPTAATLHAMHYHKIDVQARQVELAKREKASIDDILTIPLAQDTNWSEEEKRNELDNN 600
           VPSPTAA LHA+HYHK+DV ARQ ELAKR +AS+DDILTIPLA + +W+ E+ +NELDNN
Sbjct: 540 VPSPTAAALHALHYHKVDVFARQAELAKRARASVDDILTIPLAVNPDWTAEQIKNELDNN 599

Query: 601 SQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKDQVVES 660
           +QGILGY+VRW++QGVGCSKVPDINDI LMEDRATLRISSQH+ANW+RHG+VT+DQV+ES
Sbjct: 600 AQGILGYVVRWIDQGVGCSKVPDINDIGLMEDRATLRISSQHIANWLRHGIVTEDQVMES 659

Query: 661 LKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHRRRREF 720
           LKRMAPVVDRQN  DPLYRP+AP+FD+++AFQAA+ELV+EGTKQPNGYTEPVLHRRRREF
Sbjct: 660 LKRMAPVVDRQNASDPLYRPLAPNFDSNIAFQAAVELVVEGTKQPNGYTEPVLHRRRREF 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: 1661
Number of extensions: 53
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 Pf1N1B4_2478 (Malate synthase G (EC 2.3.3.9))
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.446199.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 1217.7   1.3          0 1217.4   1.3    1.0  1  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2478  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2478  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1217.4   1.3         0         0       2     720 ..       4     722 ..       3     723 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1217.4 bits;  conditional E-value: 0
                                  TIGR01345   2 rvdagrlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaideyhrkn 69 
                                                +v++g+lqvak+l dfv++e++pgtg+ a+ fw+g d++++dlap+n+ llakrd++qa id++h+  
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2478   4 HVQVGGLQVAKVLFDFVNNEAIPGTGLTADTFWAGADKVIHDLAPKNKALLAKRDDFQARIDAWHQAR 71 
                                                6899**************************************************************** PP

                                  TIGR01345  70 kgv.idkeayksflkeigylveepervtietenvdseiasqagpqlvvpvlnaryalnaanarwgsly 136
                                                 gv  d  ayk fl++igyl +e    + +t+nvd+eia  agpqlvvpv+nar+alna+narwgsly
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2478  72 AGVaHDAVAYKAFLQDIGYLLPEAADFQATTQNVDDEIARMAGPQLVVPVMNARFALNASNARWGSLY 139
                                                97527999************************************************************ PP

                                  TIGR01345 137 dalygsnvipeedgaekgkeynpkrgekviefarefldeslplesgsyadvvkykivdkklavqlesg 204
                                                dalyg+++i+e dgaekgk yn +rg+kvi+far flde+ pl +gs+ d   yki+d+kl+v l+ g
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2478 140 DALYGTDAISEADGAEKGKGYNKVRGDKVIAFARAFLDEAAPLAAGSHVDSTGYKIIDGKLVVALKGG 207
                                                ******************************************************************** PP

                                  TIGR01345 205 kvtrlkdeeqfvgyrgdaadpevillktnglhielqidarhpigkadkakvkdivlesaittildced 272
                                                + t l+d++q +g++gd+a+p++illk+nglh e+qida  p+g++d a+vkdi++e+a+tti+dced
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2478 208 SNTGLRDDAQLIGFHGDTAAPTAILLKNNGLHFEIQIDASTPVGQTDAAGVKDILMEAALTTIMDCED 275
                                                ******************************************************************** PP

                                  TIGR01345 273 svaavdaedkvlvyrnllglmkgtlkeklekngriikrklnedrsytaangeelslhgrsllfvrnvg 340
                                                svaavda+dkv++yrn+lglmkg+l e+++k g++++r +n dr+yta +g+elslhgrsllfvrnvg
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2478 276 SVAAVDADDKVVIYRNWLGLMKGDLSEEVSKGGQTFTRTMNADRTYTALDGSELSLHGRSLLFVRNVG 343
                                                ******************************************************************** PP

                                  TIGR01345 341 hlmtipviltdegeeipegildgvltsvialydlkvqnklrnsrkgsvyivkpkmhgpeevafanklf 408
                                                hlmti +il+++g+e+pegildg++t++ a++ l+ +++ +nsr+gsvyivkpkmhgpee af+n+lf
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2478 344 HLMTIDAILDKDGNEVPEGILDGLVTCLAAIHSLNGNSSRKNSRTGSVYIVKPKMHGPEEAAFTNELF 411
                                                ******************************************************************** PP

                                  TIGR01345 409 triedllglerhtlkvgvmdeerrtslnlkaciakvkervafintgfldrtgdeihtsmeagamvrka 476
                                                +ried+lgl+r+tlkvg+mdeerrt++nlkaci+ ++erv+fintgfldrtgdeihtsmeag+mvrka
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2478 412 GRIEDVLGLPRNTLKVGIMDEERRTTVNLKACIKAAAERVVFINTGFLDRTGDEIHTSMEAGPMVRKA 479
                                                ******************************************************************** PP

                                  TIGR01345 477 dmksapwlkayernnvaagltcglrgkaqigkgmwampdlmaemlekkgdqlragantawvpsptaat 544
                                                dmk+  w++aye+ nv+ gl +gl+g+aqigkgmwampdlma mle+k+  + agantawvpsptaa+
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2478 480 DMKAEKWISAYENWNVDIGLSTGLQGRAQIGKGMWAMPDLMAAMLEQKIAHPMAGANTAWVPSPTAAA 547
                                                ******************************************************************** PP

                                  TIGR01345 545 lhalhyhrvdvqkvqkeladaerraelkeiltipvaentnwseeeikeeldnnvqgilgyvvrwveqg 612
                                                lhalhyh+vdv++ q+ela+   ra+ ++iltip+a n +w++e+ik+eldnn+qgilgyvvrw++qg
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2478 548 LHALHYHKVDVFARQAELAKR-ARASVDDILTIPLAVNPDWTAEQIKNELDNNAQGILGYVVRWIDQG 614
                                                *******************99.899******************************************* PP

                                  TIGR01345 613 igcskvpdihnvalmedratlrissqhlanwlrhgivskeqvleslermakvvdkqnagdeayrpmad 680
                                                +gcskvpdi ++ lmedratlrissqh+anwlrhgiv+ +qv+esl+rma vvd+qna d+ yrp+a+
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2478 615 VGCSKVPDINDIGLMEDRATLRISSQHIANWLRHGIVTEDQVMESLKRMAPVVDRQNASDPLYRPLAP 682
                                                ******************************************************************** PP

                                  TIGR01345 681 nleasvafkaakdlilkgtkqpsgytepilharrlefkek 720
                                                n+++ +af+aa +l+++gtkqp+gytep+lh+rr+efk+ 
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2478 683 NFDSNIAFQAAVELVVEGTKQPNGYTEPVLHRRRREFKAA 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 29.74
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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 2024 update 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