GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS24015 in Pseudomonas stutzeri RCH2

Align ABC transporter related (characterized, see rationale)
to candidate GFF4241 Psest_4314 ABC-type metal ion transport system, ATPase component

Query= uniprot:B2TBJ9
         (263 letters)



>FitnessBrowser__psRCH2:GFF4241
          Length = 335

 Score =  154 bits (388), Expect = 3e-42
 Identities = 96/247 (38%), Positives = 139/247 (56%), Gaps = 17/247 (6%)

Query: 14  IHKSFG----DHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGSVSLAG 69
           +HK++     D   L+   L+   G+V  ++G SG+GKST LR +N LE P  G + + G
Sbjct: 7   VHKTYRTGGRDVPALQPTQLEIASGEVFGLIGHSGAGKSTLLRLINRLEEPSGGRILVNG 66

Query: 70  EELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRVQK-RSR 128
           E++             D   + R R ++GM+FQ+FNL    TV +N +  P+R+   RSR
Sbjct: 67  EDVTAL----------DADGLRRFRQRVGMIFQHFNLLMSKTVADN-VAMPLRLAGIRSR 115

Query: 129 AESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSALDPE 188
            E      ALL +VGL E    YPA LSGGQ+QRV IARALA  P ++L DE TSALDP+
Sbjct: 116 REIDARVAALLERVGLKEHARKYPAQLSGGQKQRVGIARALATEPSILLCDEATSALDPQ 175

Query: 189 LVGEVLRVMRSLAEEGR-TMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVFVECKS 247
               VL+++  +  E + T++++THEM   R V +RV  +  G +   G   EVF+  K 
Sbjct: 176 TTASVLQLLAEINRELKLTIVLITHEMDVIRRVCDRVAVMDAGAIVEQGPVTEVFLHPKH 235

Query: 248 DRFRQFV 254
              ++FV
Sbjct: 236 PTTQRFV 242


Lambda     K      H
   0.318    0.133    0.377 

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: 206
Number of extensions: 11
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: 263
Length of database: 335
Length adjustment: 26
Effective length of query: 237
Effective length of database: 309
Effective search space:    73233
Effective search space used:    73233
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: 48 (23.1 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