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_085773913.1 B1812_RS21530 ABC transporter ATP-binding protein

Query= uniprot:D8IUY7
         (241 letters)



>NCBI__GCF_002117405.1:WP_085773913.1
          Length = 251

 Score = 81.6 bits (200), Expect = 1e-20
 Identities = 58/194 (29%), Positives = 97/194 (50%), Gaps = 15/194 (7%)

Query: 18  IQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGHIEYLGQPLKGKKSF 77
           + A++G+  E+  GE V ++GA+G+GK+T L  + G L      G I   G+ +      
Sbjct: 33  VPALRGVSFEIERGEFVAIMGASGSGKSTLLNLL-GALDKPTA-GEIVIDGESVSAMGDD 90

Query: 78  ELV---KDKLAMVPEGRGVFTRMSIQENLLMGAYTSDDKGQIAADIDKWFAVFPRLKE-- 132
           EL      K+  V +   +  RMS  EN+L+    S + G     +DK      RL E  
Sbjct: 91  ELAALRSRKIGFVFQQFNLLPRMSALENVLLPLNYSREVG-----LDKKALALARLAEMG 145

Query: 133 ---RAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIFEVIRNVSAQ 189
              R       LSGG+QQ +A+ARAL++ P L+L DEP+  L     ++I  +   +  +
Sbjct: 146 LEARVHHRPSQLSGGQQQRVAIARALVNGPSLVLADEPTGALDTQTSQEIMRLFSELHVK 205

Query: 190 GITILLVEQNAKLA 203
           G+T++++    ++A
Sbjct: 206 GLTVIVITHEPEVA 219


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: 144
Number of extensions: 6
Number of successful extensions: 2
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: 251
Length adjustment: 24
Effective length of query: 217
Effective length of database: 227
Effective search space:    49259
Effective search space used:    49259
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