Alignments for a candidate for glcB in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for glcB in Pseudomonas stutzeri RCH2

Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate GFF353 Psest_0354 malate synthase G

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



>FitnessBrowser__psRCH2:GFF353
          Length = 726

 Score = 1449 bits (3751), Expect = 0.0
 Identities = 726/726 (100%), Positives = 726/726 (100%)

Query: 1   MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60
           MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL
Sbjct: 1   MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60

Query: 61  QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120
           QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP
Sbjct: 61  QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120

Query: 121 IMNARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAA 180
           IMNARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAA
Sbjct: 121 IMNARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAA 180

Query: 181 PLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHF 240
           PLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHF
Sbjct: 181 PLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHF 240

Query: 241 EIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDL 300
           EIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDL
Sbjct: 241 EIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDL 300

Query: 301 VEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEV 360
           VEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEV
Sbjct: 301 VEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEV 360

Query: 361 PEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLG 420
           PEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLG
Sbjct: 361 PEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLG 420

Query: 421 LPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVRKA 480
           LPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVRKA
Sbjct: 421 LPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVRKA 480

Query: 481 AMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTAW 540
           AMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTAW
Sbjct: 481 AMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTAW 540

Query: 541 VPSPTAATLHAMHYHKIDVQARQVELAKREKASIDDILTIPLAQDTNWSEEEKRNELDNN 600
           VPSPTAATLHAMHYHKIDVQARQVELAKREKASIDDILTIPLAQDTNWSEEEKRNELDNN
Sbjct: 541 VPSPTAATLHAMHYHKIDVQARQVELAKREKASIDDILTIPLAQDTNWSEEEKRNELDNN 600

Query: 601 SQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKDQVVES 660
           SQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKDQVVES
Sbjct: 601 SQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKDQVVES 660

Query: 661 LKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHRRRREF 720
           LKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHRRRREF
Sbjct: 661 LKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHRRRREF 720

Query: 721 KAKNGL 726
           KAKNGL
Sbjct: 721 KAKNGL 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: 1800
Number of extensions: 47
Number of successful extensions: 1
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: 726
Length adjustment: 40
Effective length of query: 686
Effective length of database: 686
Effective search space:   470596
Effective search space used:   470596
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 GFF353 Psest_0354 (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.5358.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 1227.1   1.8          0 1226.9   1.8    1.0  1  lcl|FitnessBrowser__psRCH2:GFF353  Psest_0354 malate synthase G


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF353  Psest_0354 malate synthase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1226.9   1.8         0         0       2     721 .]       4     724 ..       3     724 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1226.9 bits;  conditional E-value: 0
                          TIGR01345   2 rvdagrlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaideyhrknk.gvidke 76 
                                        rv++g+lqvak+l+dfv++e++pgtgvda++fw+g d +++dlap+nr llakrd++qa id++h+     + d  
  lcl|FitnessBrowser__psRCH2:GFF353   4 RVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDLQAQIDAWHQARAgQAHDAV 79 
                                        789****************************************************************99557899* PP

                          TIGR01345  77 ayksflkeigylveepervtietenvdseiasqagpqlvvpvlnaryalnaanarwgslydalygsnvipeedgae 152
                                        ayksfl+eigyl +e e  + +tenvd+eia  agpqlvvp++nar+alnaanarwgslydalyg+++i+e dga 
  lcl|FitnessBrowser__psRCH2:GFF353  80 AYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVPIMNARFALNAANARWGSLYDALYGTDAISEADGAS 155
                                        **************************************************************************** PP

                          TIGR01345 153 kgkeynpkrgekviefarefldeslplesgsyadvvkykivdkklavqlesgkvtrlkdeeqfvgyrgdaadpevi 228
                                        kg  yn  rg+kvi++ar+fl+e+ ple+gs+ d   y+i  +kl+v l++g++t lk+++q +g++g+a++p ++
  lcl|FitnessBrowser__psRCH2:GFF353 156 KGPGYNEIRGNKVIAYARNFLNEAAPLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAV 231
                                        **************************************************************************** PP

                          TIGR01345 229 llktnglhielqidarhpigkadkakvkdivlesaittildcedsvaavdaedkvlvyrnllglmkgtlkeklekn 304
                                        llk+ng+h e+qid+  pig++d a+vkdi++esa+tti+dceds+aavda+dk++vyrn+lglmkg+l e+lek 
  lcl|FitnessBrowser__psRCH2:GFF353 232 LLKNNGIHFEIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDLVEELEKG 307
                                        **************************************************************************** PP

                          TIGR01345 305 griikrklnedrsytaange.elslhgrsllfvrnvghlmtipviltdegeeipegildgvltsvialydlkvqnk 379
                                        g+ i+r +n dr+yt a+g+ el+lhgrsllf+rnvghlmt+ +il++eg+e+pegi+dg++ts+ia+++l+ + +
  lcl|FitnessBrowser__psRCH2:GFF353 308 GKRITRAMNPDRVYTKADGNgELTLHGRSLLFIRNVGHLMTNDAILDKEGNEVPEGIMDGLFTSLIAVHNLNGNTS 383
                                        ******************9769****************************************************** PP

                          TIGR01345 380 lrnsrkgsvyivkpkmhgpeevafanklftriedllglerhtlkvgvmdeerrtslnlkaciakvkervafintgf 455
                                         +n+r+gs+yivkpkmhgpeevafa +lf+r+ed+lgl+r+tlkvg+mdeerrt++nlkaci++++erv+fintgf
  lcl|FitnessBrowser__psRCH2:GFF353 384 RKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLGLPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGF 459
                                        **************************************************************************** PP

                          TIGR01345 456 ldrtgdeihtsmeagamvrkadmksapwlkayernnvaagltcglrgkaqigkgmwampdlmaemlekkgdqlrag 531
                                        ldrtgdeihtsmeag+mvrka mk+  w++aye+nnv+ gl cgl+gkaqigkgmwampdlma mle+k++ + ag
  lcl|FitnessBrowser__psRCH2:GFF353 460 LDRTGDEIHTSMEAGPMVRKAAMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAG 535
                                        **************************************************************************** PP

                          TIGR01345 532 antawvpsptaatlhalhyhrvdvqkvqkeladaerraelkeiltipvaentnwseeeikeeldnnvqgilgyvvr 607
                                        antawvpsptaatlha+hyh+ dvq+ q ela+  ++a++++iltip+a++tnwseee+++eldnn qgilgy+vr
  lcl|FitnessBrowser__psRCH2:GFF353 536 ANTAWVPSPTAATLHAMHYHKIDVQARQVELAKR-EKASIDDILTIPLAQDTNWSEEEKRNELDNNSQGILGYMVR 610
                                        ********************************99.7899************************************* PP

                          TIGR01345 608 wveqgigcskvpdihnvalmedratlrissqhlanwlrhgivskeqvleslermakvvdkqnagdeayrpmadnle 683
                                        wveqg+gcskvpdi ++almedratlrissqh+anw+rhg+v+k+qv+esl+rma vvd+qn gd+ yrpma++++
  lcl|FitnessBrowser__psRCH2:GFF353 611 WVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKDQVVESLKRMAPVVDRQNQGDPLYRPMAPDFD 686
                                        **************************************************************************** PP

                          TIGR01345 684 asvafkaakdlilkgtkqpsgytepilharrlefkekn 721
                                        +svaf+aa +l+l+gtkqp+gytep+lh+rr+efk+kn
  lcl|FitnessBrowser__psRCH2:GFF353 687 NSVAFQAALELVLEGTKQPNGYTEPVLHRRRREFKAKN 724
                                        ***********************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (721 nodes)
Target sequences:                          1  (726 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: 00:00:00.06
# Mc/sec: 8.36
//
[ok]

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

Downloads

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

Related tools

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