Alignments for a candidate for liuB in Pseudomonas stutzeri A1501

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Pseudomonas stutzeri A1501

Align Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4) (characterized)
to candidate WP_011914289.1 PST_RS16135 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

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



>NCBI__GCF_000013785.1:WP_011914289.1
          Length = 636

 Score =  982 bits (2539), Expect = 0.0
 Identities = 496/646 (76%), Positives = 553/646 (85%), Gaps = 14/646 (2%)

Query: 6   LTTLLVANRGEIACRVMRTAKALGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYL 65
           + TLLVANRGEIACRVMRTAKA+GLTTVAVHSA D  ARH+READIR+DLGG+K A+SYL
Sbjct: 5   IDTLLVANRGEIACRVMRTAKAMGLTTVAVHSAIDASARHAREADIRIDLGGAKPAESYL 64

Query: 66  QIDKLIAAAKASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSKSAAKA 125
           +IDKLI AAKASGAQAIHPGYGFLSENA FARAIE AGLIFLGPPASAIDAMGSKSAAKA
Sbjct: 65  RIDKLIEAAKASGAQAIHPGYGFLSENAEFARAIEQAGLIFLGPPASAIDAMGSKSAAKA 124

Query: 126 LMETAGVPLVPGYHGEAQDLETFRDACERIGYPVLLKATAGGGGKGMKVVEDVSQLAEAL 185
           LME AGVPLVPGYHGEAQD+ETFR A E+IGYPVLLKATAGGGGKGMKVVE  + LAEAL
Sbjct: 125 LMEEAGVPLVPGYHGEAQDVETFRAAAEKIGYPVLLKATAGGGGKGMKVVEREADLAEAL 184

Query: 186 ASAQREALSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEE 245
           ASAQREA SSFGDSRMLVEKY+LKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEE
Sbjct: 185 ASAQREAQSSFGDSRMLVEKYVLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEE 244

Query: 246 APAPGLSPELRRAMGEAAVRSAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTE 305
           APAPGLSPELRRAMGEAAV++A+AIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTE
Sbjct: 245 APAPGLSPELRRAMGEAAVKAAKAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTE 304

Query: 306 AITGLDLVAWQIRVARGEALPMTQDQVPLIGHAIEVRLYAEDPGNDFLPATGRLALYRES 365
           AITGLDLVAWQIRVARGE LP++Q+QVPLIGHAIEVRLYAEDP NDFLPATG L LYRE+
Sbjct: 305 AITGLDLVAWQIRVARGEPLPISQEQVPLIGHAIEVRLYAEDPDNDFLPATGTLELYREA 364

Query: 366 AAGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFAIGGLKTNIN 425
           A GPGRRVDSGV EGD +SPFYDPMLGKLIAWGE+RE+ARLRLL+MLDE A+GG++TN+ 
Sbjct: 365 ADGPGRRVDSGVAEGDTVSPFYDPMLGKLIAWGENREEARLRLLAMLDETAVGGVRTNLA 424

Query: 426 FLRRIIGHPAFAAAELDTGFIPRYQEQLLPAPSDLSDEFWQAAAQAFAQSQSSTTRADDL 485
           FLRR++GH AFA AELDTGFIPR++ +LL    +LSD FWQ AA+ F QS+ ++ R DD 
Sbjct: 425 FLRRVVGHRAFAQAELDTGFIPRHESELLRPAGELSDAFWQQAAECFVQSEPTSVRDDDA 484

Query: 486 SSPWGIGNGFRAGLPTEITLHLSCEEQDRALTLGDADAHTAQLKGEYLLTEHNGLRRQHR 545
            SPW   +G R G+P +I+LHL C  + R L +  A                    R  R
Sbjct: 485 HSPWSKRSGLRFGMPAQISLHLQCNGESRRLKVDPAAPRQNV--------------RTPR 530

Query: 546 AIRRGDTLYLQWDGELRRIESYDPISAVEASHSHQGGLTAPMNGSIVRVLVEAGQTVEAG 605
           AIR+GD LYLQW+GE   + ++DPI+  EASH H GGLTAPMNGSIVRVLVEAGQ VEAG
Sbjct: 531 AIRQGDALYLQWNGEWLAVRAFDPIAEAEASHQHHGGLTAPMNGSIVRVLVEAGQHVEAG 590

Query: 606 AQLVVLEAMKMEHSIRAPHAGIIKALYCQEGEMVSEGSALVELEHA 651
             L+VLEAMKMEHSIR+  AG++K+L+C EGEMVSEG+ L+E+E A
Sbjct: 591 TALIVLEAMKMEHSIRSAQAGVVKSLFCSEGEMVSEGAVLLEMEEA 636


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: 1281
Number of extensions: 41
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: 636
Length adjustment: 38
Effective length of query: 613
Effective length of database: 598
Effective search space:   366574
Effective search space used:   366574
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 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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