Alignments for a candidate for liuB in Pseudomonas litoralis 2SM5

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Pseudomonas litoralis 2SM5

Align Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4) (characterized)
to candidate WP_090274990.1 BLU11_RS15720 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

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



>NCBI__GCF_900105005.1:WP_090274990.1
          Length = 640

 Score =  954 bits (2466), Expect = 0.0
 Identities = 487/644 (75%), Positives = 543/644 (84%), Gaps = 14/644 (2%)

Query: 6   LTTLLVANRGEIACRVMRTAKALGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYL 65
           + TLLVANRGEIACRVM TAK++GLTTVAVHSA D +ARH+READIR+DLGG+K ADSYL
Sbjct: 5   IDTLLVANRGEIACRVMSTAKSMGLTTVAVHSAVDANARHAREADIRIDLGGAKPADSYL 64

Query: 66  QIDKLIAAAKASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSKSAAKA 125
           QIDKLIAAAK+SGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPA+AIDAMGSKSAAKA
Sbjct: 65  QIDKLIAAAKSSGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPAAAIDAMGSKSAAKA 124

Query: 126 LMETAGVPLVPGYHGEAQDLETFRDACERIGYPVLLKATAGGGGKGMKVVEDVSQLAEAL 185
           LME AGVPLVPGYHGEAQDLETFR A E IGYPVLLKATAGGGGKGMKVVE    LAEAL
Sbjct: 125 LMEEAGVPLVPGYHGEAQDLETFRAAAELIGYPVLLKATAGGGGKGMKVVEREEDLAEAL 184

Query: 186 ASAQREALSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEE 245
           ASAQREA SSFGD+RMLVEKY+LKPRHVEIQ+FADQ GNCLYLNERDCSIQRRHQKVVEE
Sbjct: 185 ASAQREAQSSFGDARMLVEKYVLKPRHVEIQIFADQQGNCLYLNERDCSIQRRHQKVVEE 244

Query: 246 APAPGLSPELRRAMGEAAVRSAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTE 305
           APAPGLS ELRRAMGEAAV +A+AIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTE
Sbjct: 245 APAPGLSAELRRAMGEAAVTAARAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTE 304

Query: 306 AITGLDLVAWQIRVARGEALPMTQDQVPLIGHAIEVRLYAEDPGNDFLPATGRLALYRES 365
           AITGLDLVAWQIRVARGE LP+TQ+QVPLIGHAIEVRLYAEDP NDFLP+TG LALYRE+
Sbjct: 305 AITGLDLVAWQIRVARGEPLPITQEQVPLIGHAIEVRLYAEDPDNDFLPSTGTLALYREA 364

Query: 366 AAGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFAIGGLKTNIN 425
           A G GRRVDSGV EGD +SPFYDPMLGKLIAWGE+RE+ARLRLL+MLDE AIGG++TN+ 
Sbjct: 365 ATGAGRRVDSGVAEGDSVSPFYDPMLGKLIAWGENREEARLRLLAMLDETAIGGVRTNLA 424

Query: 426 FLRRIIGHPAFAAAELDTGFIPRYQEQLLPAPSDLSDEFWQAAAQAFAQSQSSTTRADDL 485
           FLRR++GHPAFA AELDT FIPR++  LL   S LSD FWQ AA+AF  +     R+DD 
Sbjct: 425 FLRRVVGHPAFADAELDTDFIPRHETDLLRPASKLSDTFWQQAAEAFVSTTPVVARSDDA 484

Query: 486 SSPWGIGNGFRAGLPTEITLHLSCEEQDRALTLGDADAHTAQLKGEYLLTEHNGLRRQHR 545
            SPW   +G R G+P +ITLHL C  + R + L  +   +++                 R
Sbjct: 485 HSPWSRYDGLRLGMPAQITLHLQCNGESRRVQLTTSQPSSSE--------------PLPR 530

Query: 546 AIRRGDTLYLQWDGELRRIESYDPISAVEASHSHQGGLTAPMNGSIVRVLVEAGQTVEAG 605
           AIR+ DTLYLQ  GE   + ++DPI+  + S   QGGLTAPMNGSIVRVLVEAGQ V AG
Sbjct: 531 AIRQNDTLYLQHSGEWLAVTAFDPITEAQDSLQQQGGLTAPMNGSIVRVLVEAGQHVAAG 590

Query: 606 AQLVVLEAMKMEHSIRAPHAGIIKALYCQEGEMVSEGSALVELE 649
             L+VLEAMKMEHSIR+   G++K+L+C EG+MVSEG+ L+ELE
Sbjct: 591 TALIVLEAMKMEHSIRSAQDGVVKSLFCNEGDMVSEGTVLLELE 634


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: 1229
Number of extensions: 29
Number of successful extensions: 3
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: 640
Length adjustment: 38
Effective length of query: 613
Effective length of database: 602
Effective search space:   369026
Effective search space used:   369026
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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Candidates (tab-delimited)
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