Alignments for a candidate for liuB in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Pseudomonas stutzeri RCH2

Align Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4) (characterized)
to candidate GFF1047 Psest_1080 Acetyl/propionyl-CoA carboxylase, alpha subunit

Query= reanno::pseudo1_N1B4:Pf1N1B4_3984
         (651 letters)



>FitnessBrowser__psRCH2:GFF1047
          Length = 633

 Score =  979 bits (2530), Expect = 0.0
 Identities = 494/647 (76%), Positives = 552/647 (85%), Gaps = 14/647 (2%)

Query: 5   VLTTLLVANRGEIACRVMRTAKALGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSY 64
           ++TTLLVANRGEIACRVMRTAKA+GLTTVAVHSA D  ARH+READIR+DLGG+K ADSY
Sbjct: 1   MITTLLVANRGEIACRVMRTAKAMGLTTVAVHSAIDATARHAREADIRIDLGGAKPADSY 60

Query: 65  LQIDKLIAAAKASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSKSAAK 124
           L+IDKLI AAKASGAQAIHPGYGFLSENA FARAIE AGLIFLGPPASAIDAMGSKSAAK
Sbjct: 61  LRIDKLIDAAKASGAQAIHPGYGFLSENAEFARAIEQAGLIFLGPPASAIDAMGSKSAAK 120

Query: 125 ALMETAGVPLVPGYHGEAQDLETFRDACERIGYPVLLKATAGGGGKGMKVVEDVSQLAEA 184
           ALME AGVPLVPGYHGEAQD+ETFR A E+IGYPVLLKATAGGGGKGMKVVE  + LAEA
Sbjct: 121 ALMEEAGVPLVPGYHGEAQDVETFRAAAEKIGYPVLLKATAGGGGKGMKVVEREADLAEA 180

Query: 185 LASAQREALSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVE 244
           LASAQREA SSFGD RMLVEKY+LKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVE
Sbjct: 181 LASAQREAQSSFGDWRMLVEKYVLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVE 240

Query: 245 EAPAPGLSPELRRAMGEAAVRSAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVT 304
           EAPAPGL+PELRRAMGEAAV++AQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVT
Sbjct: 241 EAPAPGLTPELRRAMGEAAVKAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVT 300

Query: 305 EAITGLDLVAWQIRVARGEALPMTQDQVPLIGHAIEVRLYAEDPGNDFLPATGRLALYRE 364
           EAITGLDLVAWQIRVARGE LP++Q+QVPLIGHAIEVRLYAEDP NDFLPATG L LYRE
Sbjct: 301 EAITGLDLVAWQIRVARGEPLPISQEQVPLIGHAIEVRLYAEDPDNDFLPATGTLDLYRE 360

Query: 365 SAAGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFAIGGLKTNI 424
           +A GPGRRVDSGV EGD +SPFYDPMLGKLIAWGE+RE+ARLRLL+MLDE A+GG++TN+
Sbjct: 361 AAEGPGRRVDSGVAEGDTVSPFYDPMLGKLIAWGENREEARLRLLAMLDETAVGGVRTNL 420

Query: 425 NFLRRIIGHPAFAAAELDTGFIPRYQEQLLPAPSDLSDEFWQAAAQAFAQSQSSTTRADD 484
            FLRR++GH AFA AELDT FIPR++ +LL    +LSD FWQ AA+ F Q++ +  R DD
Sbjct: 421 AFLRRVVGHRAFAEAELDTAFIPRHESELLRPAGELSDAFWQQAAECFVQTEPTKVRGDD 480

Query: 485 LSSPWGIGNGFRAGLPTEITLHLSCEEQDRALTLGDADAHTAQLKGEYLLTEHNGLRRQH 544
             SPW   +G R G+P +I+LHL C  + R L +  A                    R  
Sbjct: 481 AHSPWSKRSGLRFGMPAQISLHLQCNGESRRLKVDPAAPQPNV--------------RTP 526

Query: 545 RAIRRGDTLYLQWDGELRRIESYDPISAVEASHSHQGGLTAPMNGSIVRVLVEAGQTVEA 604
           +AIR+GD LYLQW+GE   + ++DPI+  EASH H GGLTAPMNGSIVRVLVEAGQ VEA
Sbjct: 527 KAIRQGDALYLQWNGEWLAVRAFDPIAEAEASHQHHGGLTAPMNGSIVRVLVEAGQHVEA 586

Query: 605 GAQLVVLEAMKMEHSIRAPHAGIIKALYCQEGEMVSEGSALVELEHA 651
           G  L+VLEAMKMEHSIR+  AG++K+L+C EGEMVSEG+ L+E+E A
Sbjct: 587 GTALIVLEAMKMEHSIRSAQAGVVKSLFCSEGEMVSEGAVLLEMEEA 633


Lambda     K      H
   0.318    0.134    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: 1261
Number of extensions: 34
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: 651
Length of database: 633
Length adjustment: 38
Effective length of query: 613
Effective length of database: 595
Effective search space:   364735
Effective search space used:   364735
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 (21.7 bits)
S2: 54 (25.4 bits)

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

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Protein sequences (fasta format)
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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 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