GapMind for catabolism of small carbon sources

 

Aligments for a candidate for liuB in Pseudomonas fluorescens FW300-N2C3

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate AO356_01595 AO356_01595 3-methylcrotonyl-CoA carboxylase

Query= reanno::pseudo5_N2C3_1:AO356_01595
         (649 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01595 AO356_01595
           3-methylcrotonyl-CoA carboxylase
          Length = 649

 Score = 1276 bits (3303), Expect = 0.0
 Identities = 649/649 (100%), Positives = 649/649 (100%)

Query: 1   MSAPALTTLLVANRGEIACRVMRTARAMGLTTVAVHSATDRDARHSREADIRVDLGGSKA 60
           MSAPALTTLLVANRGEIACRVMRTARAMGLTTVAVHSATDRDARHSREADIRVDLGGSKA
Sbjct: 1   MSAPALTTLLVANRGEIACRVMRTARAMGLTTVAVHSATDRDARHSREADIRVDLGGSKA 60

Query: 61  ADSYLQIDKLIAAAKASGAQAIHPGYGFLSENAGFARAIENAGLIFLGPPASAIDAMGSK 120
           ADSYLQIDKLIAAAKASGAQAIHPGYGFLSENAGFARAIENAGLIFLGPPASAIDAMGSK
Sbjct: 61  ADSYLQIDKLIAAAKASGAQAIHPGYGFLSENAGFARAIENAGLIFLGPPASAIDAMGSK 120

Query: 121 SAAKTLMETAGVPLVPGYHGEAQDLETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQ 180
           SAAKTLMETAGVPLVPGYHGEAQDLETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQ
Sbjct: 121 SAAKTLMETAGVPLVPGYHGEAQDLETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQ 180

Query: 181 LAEALASAQREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQ 240
           LAEALASAQREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQ
Sbjct: 181 LAEALASAQREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQ 240

Query: 241 KVVEEAPAPGLTPQLRRAMGEAAVRAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVE 300
           KVVEEAPAPGLTPQLRRAMGEAAVRAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVE
Sbjct: 241 KVVEEAPAPGLTPQLRRAMGEAAVRAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVE 300

Query: 301 HPVTEAITGLDLVAWQIRVAQGEPLPITQAQVPLLGHAIEVRLYAEDPGNDFLPATGRLA 360
           HPVTEAITGLDLVAWQIRVAQGEPLPITQAQVPLLGHAIEVRLYAEDPGNDFLPATGRLA
Sbjct: 301 HPVTEAITGLDLVAWQIRVAQGEPLPITQAQVPLLGHAIEVRLYAEDPGNDFLPATGRLA 360

Query: 361 LYRESAEGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFVIGGL 420
           LYRESAEGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFVIGGL
Sbjct: 361 LYRESAEGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFVIGGL 420

Query: 421 KTNIGFLRRIVAHPAFAAAELDTGFIPRYQAQLLPEPSELDDAFWFAAAQGVALSLAPHV 480
           KTNIGFLRRIVAHPAFAAAELDTGFIPRYQAQLLPEPSELDDAFWFAAAQGVALSLAPHV
Sbjct: 421 KTNIGFLRRIVAHPAFAAAELDTGFIPRYQAQLLPEPSELDDAFWFAAAQGVALSLAPHV 480

Query: 481 RGDDAGSPWASTTGMRLGLPRETTLHLSCEGQDRALTLDVTAHCAELEGERLTIEHHGVR 540
           RGDDAGSPWASTTGMRLGLPRETTLHLSCEGQDRALTLDVTAHCAELEGERLTIEHHGVR
Sbjct: 481 RGDDAGSPWASTTGMRLGLPRETTLHLSCEGQDRALTLDVTAHCAELEGERLTIEHHGVR 540

Query: 541 RSHRAIRQVDSLYLQWEGDLHRIDLYDPLAAAEASHSHQGGLVAPMNGSIVRVLVGVGQT 600
           RSHRAIRQVDSLYLQWEGDLHRIDLYDPLAAAEASHSHQGGLVAPMNGSIVRVLVGVGQT
Sbjct: 541 RSHRAIRQVDSLYLQWEGDLHRIDLYDPLAAAEASHSHQGGLVAPMNGSIVRVLVGVGQT 600

Query: 601 VEAGAQLVVLEAMKMEHSIRAPKAGVIKALYCQEGEMVSEGSALVAFEE 649
           VEAGAQLVVLEAMKMEHSIRAPKAGVIKALYCQEGEMVSEGSALVAFEE
Sbjct: 601 VEAGAQLVVLEAMKMEHSIRAPKAGVIKALYCQEGEMVSEGSALVAFEE 649


Lambda     K      H
   0.319    0.134    0.390 

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: 1538
Number of extensions: 36
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: 649
Length of database: 649
Length adjustment: 38
Effective length of query: 611
Effective length of database: 611
Effective search space:   373321
Effective search space used:   373321
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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