GapMind for catabolism of small carbon sources

 

Aligments for a candidate for liuD in Pseudomonas stutzeri RCH2

Align Methylcrotonyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.4) (characterized)
to candidate GFF1050 Psest_1083 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta)

Query= reanno::psRCH2:GFF1050
         (535 letters)



>lcl|FitnessBrowser__psRCH2:GFF1050 Psest_1083 Acetyl-CoA
           carboxylase, carboxyltransferase component (subunits
           alpha and beta)
          Length = 535

 Score = 1066 bits (2756), Expect = 0.0
 Identities = 535/535 (100%), Positives = 535/535 (100%)

Query: 1   MAILHTQINIRSPEFAANSAAMLEQVNDLRALLGRVSEGGGATAQQRHVSRGKLLVRERI 60
           MAILHTQINIRSPEFAANSAAMLEQVNDLRALLGRVSEGGGATAQQRHVSRGKLLVRERI
Sbjct: 1   MAILHTQINIRSPEFAANSAAMLEQVNDLRALLGRVSEGGGATAQQRHVSRGKLLVRERI 60

Query: 61  DTLLDAGSAFLELAPLAAHEVYGEDVAAAGVVAGIGRVEGIECMIIANDATVKGGTYYPL 120
           DTLLDAGSAFLELAPLAAHEVYGEDVAAAGVVAGIGRVEGIECMIIANDATVKGGTYYPL
Sbjct: 61  DTLLDAGSAFLELAPLAAHEVYGEDVAAAGVVAGIGRVEGIECMIIANDATVKGGTYYPL 120

Query: 121 TVKKHLRAQTVARENRLPCIYLVDSGGANLPRQDEVFPDREHFGRIFFNQANMSAMGIPQ 180
           TVKKHLRAQTVARENRLPCIYLVDSGGANLPRQDEVFPDREHFGRIFFNQANMSAMGIPQ
Sbjct: 121 TVKKHLRAQTVARENRLPCIYLVDSGGANLPRQDEVFPDREHFGRIFFNQANMSAMGIPQ 180

Query: 181 IAVVMGSCTAGGAYVPAMADETIMVRNQATIFLAGPPLVKAATGEVVTAEELGGADVHCK 240
           IAVVMGSCTAGGAYVPAMADETIMVRNQATIFLAGPPLVKAATGEVVTAEELGGADVHCK
Sbjct: 181 IAVVMGSCTAGGAYVPAMADETIMVRNQATIFLAGPPLVKAATGEVVTAEELGGADVHCK 240

Query: 241 TSGVADHYAENDEHALSIARRCVANLNWRKLGQLQTREPRAPLYAADELYGVIPAQAKQP 300
           TSGVADHYAENDEHALSIARRCVANLNWRKLGQLQTREPRAPLYAADELYGVIPAQAKQP
Sbjct: 241 TSGVADHYAENDEHALSIARRCVANLNWRKLGQLQTREPRAPLYAADELYGVIPAQAKQP 300

Query: 301 YDVREVIARLVDGSEFDEFKALFGTTLVCGFAHLHGYPIAILANNGILFAEAAQKGAHFI 360
           YDVREVIARLVDGSEFDEFKALFGTTLVCGFAHLHGYPIAILANNGILFAEAAQKGAHFI
Sbjct: 301 YDVREVIARLVDGSEFDEFKALFGTTLVCGFAHLHGYPIAILANNGILFAEAAQKGAHFI 360

Query: 361 ELACQRGIPLLFLQNITGFMVGQKYEAGGIAKHGAKLVTAVACAQVPKFTVLIGGSFGAG 420
           ELACQRGIPLLFLQNITGFMVGQKYEAGGIAKHGAKLVTAVACAQVPKFTVLIGGSFGAG
Sbjct: 361 ELACQRGIPLLFLQNITGFMVGQKYEAGGIAKHGAKLVTAVACAQVPKFTVLIGGSFGAG 420

Query: 421 NYGMCGRAYDPRFLWMWPNARIAVMGGEQAAGVLAQVKQEQSERAGKSLGDDEVAAIKQP 480
           NYGMCGRAYDPRFLWMWPNARIAVMGGEQAAGVLAQVKQEQSERAGKSLGDDEVAAIKQP
Sbjct: 421 NYGMCGRAYDPRFLWMWPNARIAVMGGEQAAGVLAQVKQEQSERAGKSLGDDEVAAIKQP 480

Query: 481 ILEQYERQGHPYYSSARLWDDGVIDPAQTREVLGLALSAALNAPIEPTRFGVFRM 535
           ILEQYERQGHPYYSSARLWDDGVIDPAQTREVLGLALSAALNAPIEPTRFGVFRM
Sbjct: 481 ILEQYERQGHPYYSSARLWDDGVIDPAQTREVLGLALSAALNAPIEPTRFGVFRM 535


Lambda     K      H
   0.321    0.136    0.405 

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: 1112
Number of extensions: 24
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: 535
Length of database: 535
Length adjustment: 35
Effective length of query: 500
Effective length of database: 500
Effective search space:   250000
Effective search space used:   250000
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 (21.8 bits)
S2: 52 (24.6 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 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