GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00900 in Methylocystis bryophila S285

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_085770499.1 B1812_RS04360 ABC transporter ATP-binding protein

Query= uniprot:D8IUY7
         (241 letters)



>NCBI__GCF_002117405.1:WP_085770499.1
          Length = 266

 Score =  191 bits (485), Expect = 1e-53
 Identities = 103/244 (42%), Positives = 161/244 (65%), Gaps = 6/244 (2%)

Query: 2   TTNILKVQQLSVAYG-GIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASR- 59
           T  +L+++ +  +Y   I A++ + L+V  GE+V L+GANG+GKTT L A +  L A R 
Sbjct: 4   TETLLELRDVEASYNQAIVALRDVSLKVRRGEIVALLGANGSGKTTILNATSRLLAAERG 63

Query: 60  --VEGHIEYLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYTS-DDKGQI 116
               G I + G+      + EL +  L  V EGR VF  ++++ENL  GA     ++ ++
Sbjct: 64  QITSGKILFDGRSTSKSSTAELAQKGLVQVLEGRRVFRSLTVEENLASGALARRSNRREL 123

Query: 117 AADIDKWFAVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMV 176
             D+D  + VFP+LK R   +AG LSGGEQQM A+ RA+M+HP+LL+LDEPSMGL+P++V
Sbjct: 124 RDDLDYVYGVFPQLKHRRRSLAGLLSGGEQQMTAIGRAMMTHPRLLILDEPSMGLAPLVV 183

Query: 177 EKIFEVIRNVS-AQGITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQMLDDPRVKA 235
           E+I++V+  ++  +G+++L+ EQNA +AL  AHRGYV+E+G++ ++G A  + +   VK 
Sbjct: 184 EEIYQVLGALNRMKGLSLLVAEQNAYVALRHAHRGYVVENGVVVLEGAAATLQEREDVKD 243

Query: 236 AYLG 239
            YLG
Sbjct: 244 FYLG 247


Lambda     K      H
   0.317    0.134    0.365 

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: 150
Number of extensions: 8
Number of successful extensions: 4
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: 241
Length of database: 266
Length adjustment: 24
Effective length of query: 217
Effective length of database: 242
Effective search space:    52514
Effective search space used:    52514
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 (21.6 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. 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