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 GFF3768 Psest_3837 malate synthase G

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



>FitnessBrowser__psRCH2:GFF3768
          Length = 726

 Score = 1014 bits (2621), Expect = 0.0
 Identities = 493/727 (67%), Positives = 598/727 (82%), Gaps = 9/727 (1%)

Query: 1   MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60
           MTERV +G LQVA  L  F+ +E +PG+G++AAAFW G D+++HDLAPKNR LLA+RD +
Sbjct: 1   MTERVTLGRLQVAANLQRFIEDEVLPGSGIEAAAFWQGLDALVHDLAPKNRELLAERDRM 60

Query: 61  QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120
           Q ++D WH+A  G   D  AY++FL+ IGYLLP   + +  T NVD EIA  AGPQLVVP
Sbjct: 61  QVELDTWHKANPGPIKDMAAYRAFLESIGYLLPVPGEVKIETANVDSEIATQAGPQLVVP 120

Query: 121 IMNARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAA 180
           IMNAR+ALNAANARWGSLYDALYGTDAISE  GA KGPGYNE+RG KVIAYARNFL++AA
Sbjct: 121 IMNARYALNAANARWGSLYDALYGTDAISEEGGAQKGPGYNEVRGAKVIAYARNFLDQAA 180

Query: 181 PLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHF 240
           PL  GSH D+T YR++ G+L V+L++GS TGL  P +  GFQGEA  P AVLLKNNG+H 
Sbjct: 181 PLAEGSHADATAYRVQDGQLKVTLENGSVTGLAQPEKFVGFQGEAVEPKAVLLKNNGLHV 240

Query: 241 EIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDL 300
           EIQIDP SPIGQTDAAGVKD+L+ESA++TI+DCEDS+AAVDADDK + YRNWLG+++G L
Sbjct: 241 EIQIDPNSPIGQTDAAGVKDLLVESAVSTILDCEDSVAAVDADDKVLAYRNWLGIVQGTL 300

Query: 301 VEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEV 360
            EE+ KG     R +NPDR Y+  +G GEL LHGRSLLFIRNVGHLMTN AIL ++G E+
Sbjct: 301 SEEVAKGSSSFVRRLNPDREYSAPNG-GELKLHGRSLLFIRNVGHLMTNPAILLEDGREI 359

Query: 361 PEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLG 420
           PEGIMDG+FTSLIA H+L     + N+RTGS+YIVKPKMHGP+EVAFA ELFGRVE+++G
Sbjct: 360 PEGIMDGVFTSLIAKHDLQ---RKGNSRTGSVYIVKPKMHGPKEVAFADELFGRVEELIG 416

Query: 421 LPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVRKA 480
           +PR TLK+GIMDEERRT+ NLKACI  A+ RV FINTGFLDRTGDE+HT MEAGP++RK 
Sbjct: 417 VPRYTLKMGIMDEERRTSANLKACIAAAKHRVAFINTGFLDRTGDEMHTCMEAGPVLRKG 476

Query: 481 AMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTAW 540
            MK+  WI +YE NNV VGLACGL+GKAQIGKGMWAMPDLMAAMLEQK+GHP +GANTAW
Sbjct: 477 DMKSTPWIQSYERNNVLVGLACGLRGKAQIGKGMWAMPDLMAAMLEQKIGHPKSGANTAW 536

Query: 541 VPSPTAATLHAMHYHKIDVQARQVELAKREKAS-----IDDILTIPLAQDTNWSEEEKRN 595
           VPSPT ATLHA+HYH+++VQA Q EL K + A+     ++D+L+IP+  +  WS EEK+ 
Sbjct: 537 VPSPTGATLHALHYHQVNVQAVQSELEKIDLAAERDQLLNDLLSIPVVAEDKWSAEEKQQ 596

Query: 596 ELDNNSQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKD 655
           ELDNN QGILGY+VRWVEQGVGCSKVPDI+++ LMEDRATLRISSQH+ANW+ HGVV+++
Sbjct: 597 ELDNNCQGILGYVVRWVEQGVGCSKVPDIHNVGLMEDRATLRISSQHIANWLHHGVVSRE 656

Query: 656 QVVESLKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHR 715
           QV E+L+RMA VVD+QN GDPLYR M+ D+  S+AFQAA +LV +G +QP GYTEP+LH 
Sbjct: 657 QVQETLQRMAKVVDQQNAGDPLYRAMSSDYTQSIAFQAASDLVFKGREQPAGYTEPLLHA 716

Query: 716 RRREFKA 722
            R+ +KA
Sbjct: 717 WRQRYKA 723


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: 1458
Number of extensions: 60
Number of successful extensions: 4
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 GFF3768 Psest_3837 (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.3497.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 1245.6   0.0          0 1245.4   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF3768  Psest_3837 malate synthase G


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF3768  Psest_3837 malate synthase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1245.4   0.0         0         0       2     720 ..       4     724 ..       3     725 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1245.4 bits;  conditional E-value: 0
                           TIGR01345   2 rvdagrlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaideyhrknk.gvidk 75 
                                         rv+ grlqva++l++f+e+evlpg g++a++fw+g+d++v+dlap+nrella+rd++q+ +d +h+ n+ + +d 
  lcl|FitnessBrowser__psRCH2:GFF3768   4 RVTLGRLQVAANLQRFIEDEVLPGSGIEAAAFWQGLDALVHDLAPKNRELLAERDRMQVELDTWHKANPgPIKDM 78 
                                         7899*****************************************************************6678** PP

                           TIGR01345  76 eayksflkeigylveepervtietenvdseiasqagpqlvvpvlnaryalnaanarwgslydalygsnvipeedg 150
                                         +ay+ fl+ igyl + p +v+iet nvdseia+qagpqlvvp++naryalnaanarwgslydalyg+++i+ee+g
  lcl|FitnessBrowser__psRCH2:GFF3768  79 AAYRAFLESIGYLLPVPGEVKIETANVDSEIATQAGPQLVVPIMNARYALNAANARWGSLYDALYGTDAISEEGG 153
                                         *************************************************************************** PP

                           TIGR01345 151 aekgkeynpkrgekviefarefldeslplesgsyadvvkykivdkklavqlesgkvtrlkdeeqfvgyrgdaadp 225
                                         a+kg  yn +rg kvi++ar+fld++ pl +gs+ad+ +y++ d++l+v+le+g+vt l ++e+fvg++g+a++p
  lcl|FitnessBrowser__psRCH2:GFF3768 154 AQKGPGYNEVRGAKVIAYARNFLDQAAPLAEGSHADATAYRVQDGQLKVTLENGSVTGLAQPEKFVGFQGEAVEP 228
                                         *************************************************************************** PP

                           TIGR01345 226 evillktnglhielqidarhpigkadkakvkdivlesaittildcedsvaavdaedkvlvyrnllglmkgtlkek 300
                                         +++llk+nglh+e+qid++ pig++d a+vkd+++esa++tildcedsvaavda+dkvl yrn+lg+++gtl e+
  lcl|FitnessBrowser__psRCH2:GFF3768 229 KAVLLKNNGLHVEIQIDPNSPIGQTDAAGVKDLLVESAVSTILDCEDSVAAVDADDKVLAYRNWLGIVQGTLSEE 303
                                         *************************************************************************** PP

                           TIGR01345 301 lekngriikrklnedrsytaangeelslhgrsllfvrnvghlmtipviltdegeeipegildgvltsvialydlk 375
                                         + k    ++r+ln dr+y a+ng el lhgrsllf+rnvghlmt+p+il ++g eipegi+dgv+ts+ia++dl+
  lcl|FitnessBrowser__psRCH2:GFF3768 304 VAKGSSSFVRRLNPDREYSAPNGGELKLHGRSLLFIRNVGHLMTNPAILLEDGREIPEGIMDGVFTSLIAKHDLQ 378
                                         *************************************************************************** PP

                           TIGR01345 376 vqnklrnsrkgsvyivkpkmhgpeevafanklftriedllglerhtlkvgvmdeerrtslnlkaciakvkervaf 450
                                         +++   nsr+gsvyivkpkmhgp+evafa++lf+r+e+l+g++r tlk+g+mdeerrts nlkacia +k+rvaf
  lcl|FitnessBrowser__psRCH2:GFF3768 379 RKG---NSRTGSVYIVKPKMHGPKEVAFADELFGRVEELIGVPRYTLKMGIMDEERRTSANLKACIAAAKHRVAF 450
                                         988...********************************************************************* PP

                           TIGR01345 451 intgfldrtgdeihtsmeagamvrkadmksapwlkayernnvaagltcglrgkaqigkgmwampdlmaemlekkg 525
                                         intgfldrtgde+ht+meag+++rk+dmks+pw+++yernnv+ gl cglrgkaqigkgmwampdlma mle+k+
  lcl|FitnessBrowser__psRCH2:GFF3768 451 INTGFLDRTGDEMHTCMEAGPVLRKGDMKSTPWIQSYERNNVLVGLACGLRGKAQIGKGMWAMPDLMAAMLEQKI 525
                                         *************************************************************************** PP

                           TIGR01345 526 dqlragantawvpsptaatlhalhyhrvdvqkvqkeladaerrae....lkeiltipvaentnwseeeikeeldn 596
                                         + +++gantawvpspt+atlhalhyh+v+vq+vq+el + +  ae    l+++l ipv  + +ws+ee+++eldn
  lcl|FitnessBrowser__psRCH2:GFF3768 526 GHPKSGANTAWVPSPTGATLHALHYHQVNVQAVQSELEKIDLAAErdqlLNDLLSIPVVAEDKWSAEEKQQELDN 600
                                         *************************************9876666544558999********************** PP

                           TIGR01345 597 nvqgilgyvvrwveqgigcskvpdihnvalmedratlrissqhlanwlrhgivskeqvleslermakvvdkqnag 671
                                         n+qgilgyvvrwveqg+gcskvpdihnv lmedratlrissqh+anwl hg+vs+eqv+e+l+rmakvvd+qnag
  lcl|FitnessBrowser__psRCH2:GFF3768 601 NCQGILGYVVRWVEQGVGCSKVPDIHNVGLMEDRATLRISSQHIANWLHHGVVSREQVQETLQRMAKVVDQQNAG 675
                                         *************************************************************************** PP

                           TIGR01345 672 deayrpmadnleasvafkaakdlilkgtkqpsgytepilharrlefkek 720
                                         d+ yr m++++ +s+af+aa+dl++kg +qp+gytep+lha+r+++k++
  lcl|FitnessBrowser__psRCH2:GFF3768 676 DPLYRAMSSDYTQSIAFQAASDLVFKGREQPAGYTEPLLHAWRQRYKAS 724
                                         **********************************************986 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 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 11.66
//
[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