Alignments for a candidate for glcB in Pantoea rwandensis LMG 26275

GapMind for catabolism of small carbon sources

Alignments for a candidate for glcB in Pantoea rwandensis LMG 26275

Align malate synthase A (EC 2.3.3.9) (characterized)
to candidate WP_084938092.1 HA51_RS25020 malate synthase A

Query= ecocyc::MALATE-SYNTHASE
         (533 letters)



>NCBI__GCF_002095475.1:WP_084938092.1
          Length = 532

 Score =  752 bits (1941), Expect = 0.0
 Identities = 358/522 (68%), Positives = 427/522 (81%)

Query: 11  LAFTRPYGEQEKQILTAEAVEFLTELVTHFTPQRNKLLAARIQQQQDIDNGTLPDFISET 70
           L F++P+   E+Q+LT EA++FL  LV  F P+R +LL AR Q+QQ  D G LPDF SET
Sbjct: 10  LTFSQPFSHAERQLLTPEAIDFLHTLVARFAPERERLLKARQQRQQRYDQGALPDFDSET 69

Query: 71  ASIRDADWKIRGIPADLEDRRVEITGPVERKMVINALNANVKVFMADFEDSLAPDWNKVI 130
            SIR+  W++R IP  L DRRVEITGP +RKMVINALNANV VFMADFEDSL+P W K++
Sbjct: 70  VSIRENSWQVRSIPELLRDRRVEITGPPDRKMVINALNANVNVFMADFEDSLSPTWQKLM 129

Query: 131 DGQINLRDAVNGTISYTNEAGKIYQLKPNPAVLICRVRGLHLPEKHVTWRGEAIPGSLFD 190
           +GQ+ LRDAVNGT+S+T+E GKIYQLK +PA+L+CRVRGLHL EKHV WR  AIPG LFD
Sbjct: 130 EGQLTLRDAVNGTLSFTSETGKIYQLKSDPALLMCRVRGLHLNEKHVEWRDRAIPGGLFD 189

Query: 191 FALYFFHNYQALLAKGSGPYFYLPKTQSWQEAAWWSEVFSYAEDRFNLPRGTIKATLLIE 250
           FALY FHN  ALL KG  P+FYLPKT+   E AWW E+F ++EDRF+LPRGTIKAT+LIE
Sbjct: 190 FALYLFHNVDALLEKGHAPWFYLPKTEHSSEVAWWREIFRFSEDRFDLPRGTIKATVLIE 249

Query: 251 TLPAVFQMDEILHALRDHIVGLNCGRWDYIFSYIKTLKNYPDRVLPDRQAVTMDKPFLNA 310
           TLPAVFQMDEIL  LRDH+VGLNCGRWDYIFSYIKTL  + DR+LPDRQ ++MD+PFL+A
Sbjct: 250 TLPAVFQMDEILWELRDHVVGLNCGRWDYIFSYIKTLAQHGDRILPDRQQISMDQPFLDA 309

Query: 311 YSRLLIKTCHKRGAFAMGGMAAFIPSKDEEHNNQVLNKVKADKSLEANNGHDGTWIAHPG 370
           YSRLLI+TCH+RGA AMGGM+A IPSKD E N  V+ KV+ DK+ EA NGHDGTW+AHPG
Sbjct: 310 YSRLLIRTCHRRGALAMGGMSALIPSKDAERNAWVMQKVQEDKAREAGNGHDGTWVAHPG 369

Query: 371 LADTAMAVFNDILGSRKNQLEVMREQDAPITADQLLAPCDGERTEEGMRANIRVAVQYIE 430
           LAD AMA F+  L  + NQL V R+ DAPITA++LL PC G+RTE GMRANIRVA+QY+E
Sbjct: 370 LADIAMAEFDRQLADQPNQLNVSRDHDAPITAERLLRPCRGQRTESGMRANIRVALQYLE 429

Query: 431 AWISGNGCVPIYGLMEDAATAEISRTSIWQWIHHQKTLSNGKPVTKALFRQMLGEEMKVI 490
           AWI GNGCVPI GLMEDAATAEI+RTSIWQWIHH++ L++G+ VT  LF ++L EE++ +
Sbjct: 430 AWIGGNGCVPIDGLMEDAATAEIARTSIWQWIHHKQILNDGQLVTAQLFERLLDEELQAL 489

Query: 491 ASELGEERFSQGRFDDAARLMEQITTSDELIDFLTLPGYRLL 532
            + LG+ERF+ GRF DAA LM QITT DEL+ FLTLPGYRLL
Sbjct: 490 QNHLGDERFNDGRFADAAALMAQITTDDELVSFLTLPGYRLL 531


Lambda     K      H
   0.320    0.135    0.407 

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: 871
Number of extensions: 27
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: 533
Length of database: 532
Length adjustment: 35
Effective length of query: 498
Effective length of database: 497
Effective search space:   247506
Effective search space used:   247506
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

Align candidate WP_084938092.1 HA51_RS25020 (malate synthase A)
to HMM TIGR01344 (aceB: malate synthase A (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/TIGR01344.hmm
# target sequence database:        /tmp/gapView.1260316.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01344  [M=511]
Accession:   TIGR01344
Description: malate_syn_A: malate synthase A
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.4e-234  763.7   0.0   3.9e-234  763.5   0.0    1.0  1  NCBI__GCF_002095475.1:WP_084938092.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002095475.1:WP_084938092.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  763.5   0.0  3.9e-234  3.9e-234       2     510 ..      24     531 ..      23     532 .] 0.99

  Alignments for each domain:
  == domain 1  score: 763.5 bits;  conditional E-value: 3.9e-234
                             TIGR01344   2 ltkealeflaelhrrfaerrkellarrekkqakldkgelldflpetkeireddwkvaaipadlldrrveitGP 74 
                                           lt+ea+ fl +l  rfa+ r++ll++r+++q ++d+g+l+df  et +ire++w+v +ip+ l drrveitGP
  NCBI__GCF_002095475.1:WP_084938092.1  24 LTPEAIDFLHTLVARFAPERERLLKARQQRQQRYDQGALPDFDSETVSIRENSWQVRSIPELLRDRRVEITGP 96 
                                           9************************************************************************ PP

                             TIGR01344  75 vdrkmvinalnaeakvfladfedsssPtwenvveGqinlkdairgeidftdeesgkeyalkaklavlivrprG 147
                                           +drkmvinalna+++vf+adfeds sPtw++++eGq++l+da++g+++ft+ e+gk y+lk++ a l++r+rG
  NCBI__GCF_002095475.1:WP_084938092.1  97 PDRKMVINALNANVNVFMADFEDSLSPTWQKLMEGQLTLRDAVNGTLSFTS-ETGKIYQLKSDPALLMCRVRG 168
                                           **************************************************5.99******************* PP

                             TIGR01344 148 whlkerhleidgkaisgslldfglyffhnarellkkGkGPyfylPkleshlearlwndvfllaqevlglprGt 220
                                           +hl+e+h+e  ++ai+g l+df+ly+fhn  +ll+kG+ P+fylPk e+  e+ +w ++f ++++ ++lprGt
  NCBI__GCF_002095475.1:WP_084938092.1 169 LHLNEKHVEWRDRAIPGGLFDFALYLFHNVDALLEKGHAPWFYLPKTEHSSEVAWWREIFRFSEDRFDLPRGT 241
                                           ************************************************************************* PP

                             TIGR01344 221 ikatvlietlpaafemdeilyelrehssGlncGrwdyifslikklkkaeevvlPdrdavtmdkaflnayskll 293
                                           ikatvlietlpa+f+mdeil+elr+h++GlncGrwdyifs+ik+l ++ +++lPdr+++ md++fl+ays+ll
  NCBI__GCF_002095475.1:WP_084938092.1 242 IKATVLIETLPAVFQMDEILWELRDHVVGLNCGRWDYIFSYIKTLAQHGDRILPDRQQISMDQPFLDAYSRLL 314
                                           ************************************************************************* PP

                             TIGR01344 294 iqtchrrgafalGGmaafiPikddpaaneaalekvradkereaknGhdGtwvahPdlvevalevfdevlge.p 365
                                           i+tchrrga a+GGm+a iP+k d++ n  +++kv+ dk rea nGhdGtwvahP+l+++a++ fd+ l + p
  NCBI__GCF_002095475.1:WP_084938092.1 315 IRTCHRRGALAMGGMSALIPSK-DAERNAWVMQKVQEDKAREAGNGHDGTWVAHPGLADIAMAEFDRQLADqP 386
                                           **********************.9*********************************************999* PP

                             TIGR01344 366 nqldrvrledvsitaaellevkdasrteeGlrenirvglryieawlrGsGavpiynlmedaataeisraqlwq 438
                                           nql+++r++d++ita  ll+ + ++rte G+r nirv+l+y+eaw+ G+G+vpi  lmedaataei+r+++wq
  NCBI__GCF_002095475.1:WP_084938092.1 387 NQLNVSRDHDAPITAERLLRPCRGQRTESGMRANIRVALQYLEAWIGGNGCVPIDGLMEDAATAEIARTSIWQ 459
                                           ************************************************************************* PP

                             TIGR01344 439 wikhGvvledGekvtselvrdllkeeleklkkesgkeeyakarleeaaellerlvlseeledfltlpaydel 510
                                           wi+h + l+dG+ vt++l+  ll+eel++l++++g+e++ ++r++ aa l+ ++++++el  fltlp+y  l
  NCBI__GCF_002095475.1:WP_084938092.1 460 WIHHKQILNDGQLVTAQLFERLLDEELQALQNHLGDERFNDGRFADAAALMAQITTDDELVSFLTLPGYRLL 531
                                           *********************************************************************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (511 nodes)
Target sequences:                          1  (532 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 15.07
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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