Aligments for a candidate for liuB in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Aligments for a candidate for liuB in Pseudomonas putida KT2440

Align Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4) (characterized)
to candidate PP_4067 PP_4067 methylcrotonyl-CoA carboxylase biotin-containing subunit alpha

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



>FitnessBrowser__Putida:PP_4067
          Length = 650

 Score = 1062 bits (2747), Expect = 0.0
 Identities = 539/648 (83%), Positives = 581/648 (89%)

Query: 1   MSAPVLTTLLVANRGEIACRVMRTAKALGLTTVAVHSATDRDARHSREADIRVDLGGSKA 60
           MS P LTTLLVANRGEIACRVMRTAKA+GLTTVAVHSATDRDARHSREADIRVDLGG+KA
Sbjct: 1   MSRPALTTLLVANRGEIACRVMRTAKAMGLTTVAVHSATDRDARHSREADIRVDLGGTKA 60

Query: 61  ADSYLQIDKLIAAAKASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSK 120
           A+SYL +DKL+AAAKASGAQAIHPGYGFLSENAGFARAIE AGLIFLGPPASAIDAMGSK
Sbjct: 61  AESYLLVDKLLAAAKASGAQAIHPGYGFLSENAGFARAIEQAGLIFLGPPASAIDAMGSK 120

Query: 121 SAAKALMETAGVPLVPGYHGEAQDLETFRDACERIGYPVLLKATAGGGGKGMKVVEDVSQ 180
           SAAKALME AGVPLVPGYHGEAQDL+TFR A ERIGYPVLLKA+AGGGGKGMKVVE+ SQ
Sbjct: 121 SAAKALMEAAGVPLVPGYHGEAQDLDTFRAAAERIGYPVLLKASAGGGGKGMKVVEEESQ 180

Query: 181 LAEALASAQREALSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQ 240
           LA+ALASAQREA SSFGD+RMLVEKY+LKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQ
Sbjct: 181 LADALASAQREAQSSFGDARMLVEKYVLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQ 240

Query: 241 KVVEEAPAPGLSPELRRAMGEAAVRSAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVE 300
           KVVEEAPAPGLSPELRRAMGEAAVR+AQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVE
Sbjct: 241 KVVEEAPAPGLSPELRRAMGEAAVRAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVE 300

Query: 301 HPVTEAITGLDLVAWQIRVARGEALPMTQDQVPLIGHAIEVRLYAEDPGNDFLPATGRLA 360
           HPVTEAITGLDLVAWQIRVA GEALP+TQ+QVPLIGHAIEVRLYAEDP NDFLPATG+LA
Sbjct: 301 HPVTEAITGLDLVAWQIRVACGEALPITQEQVPLIGHAIEVRLYAEDPANDFLPATGKLA 360

Query: 361 LYRESAAGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFAIGGL 420
           LYRESA G GRRVDSGV EGD +SPFYDPMLGKLIAWGEDREQARLRLL+MLDEFAIGGL
Sbjct: 361 LYRESAPGEGRRVDSGVSEGDVVSPFYDPMLGKLIAWGEDREQARLRLLAMLDEFAIGGL 420

Query: 421 KTNINFLRRIIGHPAFAAAELDTGFIPRYQEQLLPAPSDLSDEFWQAAAQAFAQSQSSTT 480
           KTNI FLRRI+ HPAFAAAELDTGFIPR+Q+ LLPAP  L   FW+AAA+A+ Q Q+   
Sbjct: 421 KTNIAFLRRILAHPAFAAAELDTGFIPRHQDVLLPAPRALPAAFWEAAAEAWLQGQAGHQ 480

Query: 481 RADDLSSPWGIGNGFRAGLPTEITLHLSCEEQDRALTLGDADAHTAQLKGEYLLTEHNGL 540
           R DD  SPW   NG R GLP   +LHL    QD+A+ L  + A T QL+GE L+ + NG+
Sbjct: 481 REDDRHSPWSGSNGLRLGLPARSSLHLVSAGQDQAVALERSAASTWQLQGEQLVHDQNGV 540

Query: 541 RRQHRAIRRGDTLYLQWDGELRRIESYDPISAVEASHSHQGGLTAPMNGSIVRVLVEAGQ 600
           RRQH AIRRG TLYL W+GE+  IE++DPI+  EASHSHQGGL APMNGSIVRVLVE GQ
Sbjct: 541 RRQHLAIRRGGTLYLHWEGEMHAIEAFDPIAEAEASHSHQGGLGAPMNGSIVRVLVEPGQ 600

Query: 601 TVEAGAQLVVLEAMKMEHSIRAPHAGIIKALYCQEGEMVSEGSALVEL 648
            VEAG  L+VLEAMKMEHSIRAPHAG +KAL+C EG+MVSEG+ LVEL
Sbjct: 601 VVEAGTALLVLEAMKMEHSIRAPHAGTVKALFCLEGDMVSEGTVLVEL 648


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: 1376
Number of extensions: 45
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: 651
Length of database: 650
Length adjustment: 38
Effective length of query: 613
Effective length of database: 612
Effective search space:   375156
Effective search space used:   375156
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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Candidates (tab-delimited)
Steps (tab-delimited)
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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 paper from 2022 on GapMind for carbon sources, or view the source code.

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