Alignments for a candidate for glcB in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for glcB in Klebsiella michiganensis M5al

Align malate synthase A (EC 2.3.3.9) (characterized)
to candidate BWI76_RS01660 BWI76_RS01660 malate synthase A

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



>FitnessBrowser__Koxy:BWI76_RS01660
          Length = 533

 Score =  990 bits (2559), Expect = 0.0
 Identities = 481/533 (90%), Positives = 508/533 (95%)

Query: 1   MTEQATTTDELAFTRPYGEQEKQILTAEAVEFLTELVTHFTPQRNKLLAARIQQQQDIDN 60
           MT+QAT TDELAF++PYG+QEKQILT EAVEFLTELV+ FTP+RN+LLAARIQQQQ ID+
Sbjct: 1   MTQQATITDELAFSQPYGDQEKQILTPEAVEFLTELVSRFTPERNRLLAARIQQQQAIDD 60

Query: 61  GTLPDFISETASIRDADWKIRGIPADLEDRRVEITGPVERKMVINALNANVKVFMADFED 120
           G LPDFISETASIR+++WKIRGIP DL+DRRVEITGPVERKMVINALNANVKVFMADFED
Sbjct: 61  GKLPDFISETASIRNSEWKIRGIPEDLQDRRVEITGPVERKMVINALNANVKVFMADFED 120

Query: 121 SLAPDWNKVIDGQINLRDAVNGTISYTNEAGKIYQLKPNPAVLICRVRGLHLPEKHVTWR 180
           SLAP+WNKVIDGQINLRDAVNGTISYTNEAGKIYQLKPNPA+LICRVRGLHLPEKHVTWR
Sbjct: 121 SLAPEWNKVIDGQINLRDAVNGTISYTNEAGKIYQLKPNPALLICRVRGLHLPEKHVTWR 180

Query: 181 GEAIPGSLFDFALYFFHNYQALLAKGSGPYFYLPKTQSWQEAAWWSEVFSYAEDRFNLPR 240
           GEAIPGSLFDFALYFFHNY+ALL KGSGPYFYLPKTQ+WQEAAWWSEVFS+ EDRF LPR
Sbjct: 181 GEAIPGSLFDFALYFFHNYKALLEKGSGPYFYLPKTQAWQEAAWWSEVFSFTEDRFELPR 240

Query: 241 GTIKATLLIETLPAVFQMDEILHALRDHIVGLNCGRWDYIFSYIKTLKNYPDRVLPDRQA 300
           GT+KATLLIETLPAVFQMDEILHALRDHIVGLNCGRWDYIFSYIKTLKN+PDRVLPDRQ 
Sbjct: 241 GTVKATLLIETLPAVFQMDEILHALRDHIVGLNCGRWDYIFSYIKTLKNHPDRVLPDRQV 300

Query: 301 VTMDKPFLNAYSRLLIKTCHKRGAFAMGGMAAFIPSKDEEHNNQVLNKVKADKSLEANNG 360
           VTMDKPFL+AYSRLLIKTCHKRGAFAMGGMAAFIPSKD E NNQVLNKVKADKSLEANNG
Sbjct: 301 VTMDKPFLSAYSRLLIKTCHKRGAFAMGGMAAFIPSKDAERNNQVLNKVKADKSLEANNG 360

Query: 361 HDGTWIAHPGLADTAMAVFNDILGSRKNQLEVMREQDAPITADQLLAPCDGERTEEGMRA 420
           HDGTWIAHPGLADTAMAVFN +LG  KNQL V RE DAPITA+QLLAPC+GERTEEGMRA
Sbjct: 361 HDGTWIAHPGLADTAMAVFNGVLGENKNQLSVTREDDAPITAEQLLAPCEGERTEEGMRA 420

Query: 421 NIRVAVQYIEAWISGNGCVPIYGLMEDAATAEISRTSIWQWIHHQKTLSNGKPVTKALFR 480
           NIRVAVQYIEAWISGNGCVPIYGLMEDAATAEISRTSIWQWIHH+KTLSNG PVTKALFR
Sbjct: 421 NIRVAVQYIEAWISGNGCVPIYGLMEDAATAEISRTSIWQWIHHEKTLSNGTPVTKALFR 480

Query: 481 QMLGEEMKVIASELGEERFSQGRFDDAARLMEQITTSDELIDFLTLPGYRLLA 533
           Q L EEM+VI  ELGE R+S GRFD+AARLMEQITTSDELIDFLTLPGYRLLA
Sbjct: 481 QWLAEEMRVIQDELGEHRYSSGRFDEAARLMEQITTSDELIDFLTLPGYRLLA 533


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: 1035
Number of extensions: 30
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: 533
Length adjustment: 35
Effective length of query: 498
Effective length of database: 498
Effective search space:   248004
Effective search space used:   248004
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 BWI76_RS01660 BWI76_RS01660 (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.4131.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   9.3e-254  828.2   0.0     1e-253  828.1   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS01660  BWI76_RS01660 malate synthase A


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS01660  BWI76_RS01660 malate synthase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  828.1   0.0    1e-253    1e-253       1     510 [.      24     532 ..      24     533 .] 0.99

  Alignments for each domain:
  == domain 1  score: 828.1 bits;  conditional E-value: 1e-253
                               TIGR01344   1 vltkealeflaelhrrfaerrkellarrekkqakldkgelldflpetkeireddwkvaaipadlldrrvei 71 
                                             +lt+ea+efl+el  rf++ r++lla+r ++q ++d g+l+df+ et++ir+++wk+  ip+dl+drrvei
  lcl|FitnessBrowser__Koxy:BWI76_RS01660  24 ILTPEAVEFLTELVSRFTPERNRLLAARIQQQQAIDDGKLPDFISETASIRNSEWKIRGIPEDLQDRRVEI 94 
                                             89********************************************************************* PP

                               TIGR01344  72 tGPvdrkmvinalnaeakvfladfedsssPtwenvveGqinlkdairgeidftdeesgkeyalkaklavli 142
                                             tGPv+rkmvinalna++kvf+adfeds +P w++v++Gqinl+da++g+i++t+ e+gk y+lk++ a li
  lcl|FitnessBrowser__Koxy:BWI76_RS01660  95 TGPVERKMVINALNANVKVFMADFEDSLAPEWNKVIDGQINLRDAVNGTISYTN-EAGKIYQLKPNPALLI 164
                                             *****************************************************7.99************** PP

                               TIGR01344 143 vrprGwhlkerhleidgkaisgslldfglyffhnarellkkGkGPyfylPkleshlearlwndvfllaqev 213
                                             +r+rG+hl+e+h++  g+ai+gsl+df+lyffhn ++ll+kG+GPyfylPk ++++ea +w++vf ++++ 
  lcl|FitnessBrowser__Koxy:BWI76_RS01660 165 CRVRGLHLPEKHVTWRGEAIPGSLFDFALYFFHNYKALLEKGSGPYFYLPKTQAWQEAAWWSEVFSFTEDR 235
                                             *********************************************************************** PP

                               TIGR01344 214 lglprGtikatvlietlpaafemdeilyelrehssGlncGrwdyifslikklkkaeevvlPdrdavtmdka 284
                                             ++lprGt+kat+lietlpa+f+mdeil+ lr+h++GlncGrwdyifs+ik+lk+++++vlPdr++vtmdk+
  lcl|FitnessBrowser__Koxy:BWI76_RS01660 236 FELPRGTVKATLLIETLPAVFQMDEILHALRDHIVGLNCGRWDYIFSYIKTLKNHPDRVLPDRQVVTMDKP 306
                                             *********************************************************************** PP

                               TIGR01344 285 flnaysklliqtchrrgafalGGmaafiPikddpaaneaalekvradkereaknGhdGtwvahPdlveval 355
                                             fl+ays+lli+tch+rgafa+GGmaafiP+k d++ n+++l+kv+adk +ea+nGhdGtw+ahP+l+++a+
  lcl|FitnessBrowser__Koxy:BWI76_RS01660 307 FLSAYSRLLIKTCHKRGAFAMGGMAAFIPSK-DAERNNQVLNKVKADKSLEANNGHDGTWIAHPGLADTAM 376
                                             *******************************.9************************************** PP

                               TIGR01344 356 evfdevlge.pnqldrvrledvsitaaellevkdasrteeGlrenirvglryieawlrGsGavpiynlmed 425
                                             +vf+ vlge +nql+++r++d++ita +ll+ ++++rteeG+r nirv+++yieaw++G+G+vpiy lmed
  lcl|FitnessBrowser__Koxy:BWI76_RS01660 377 AVFNGVLGEnKNQLSVTREDDAPITAEQLLAPCEGERTEEGMRANIRVAVQYIEAWISGNGCVPIYGLMED 447
                                             ********99************************************************************* PP

                               TIGR01344 426 aataeisraqlwqwikhGvvledGekvtselvrdllkeeleklkkesgkeeyakarleeaaellerlvlse 496
                                             aataeisr+++wqwi+h ++l++G  vt++l+r+ l+ee+  +++e+g+++y+++r++eaa+l+e++++s+
  lcl|FitnessBrowser__Koxy:BWI76_RS01660 448 AATAEISRTSIWQWIHHEKTLSNGTPVTKALFRQWLAEEMRVIQDELGEHRYSSGRFDEAARLMEQITTSD 518
                                             *********************************************************************** PP

                               TIGR01344 497 eledfltlpaydel 510
                                             el dfltlp+y  l
  lcl|FitnessBrowser__Koxy:BWI76_RS01660 519 ELIDFLTLPGYRLL 532
                                             ***********876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (511 nodes)
Target sequences:                          1  (533 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: 00:00:00.02
# Mc/sec: 11.46
//
[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