GapMind for catabolism of small carbon sources

 

Alignments 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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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:

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:

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:

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:

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