GapMind for catabolism of small carbon sources

 

Aligments for a candidate for BPHYT_RS24015 in Pseudomonas stutzeri RCH2

Align ABC transporter related (characterized, see rationale)
to candidate GFF139 Psest_0139 ABC-type histidine transport system, ATPase component

Query= uniprot:B2TBJ9
         (263 letters)



>lcl|FitnessBrowser__psRCH2:GFF139 Psest_0139 ABC-type histidine
           transport system, ATPase component
          Length = 257

 Score =  335 bits (860), Expect = 4e-97
 Identities = 169/256 (66%), Positives = 207/256 (80%)

Query: 3   ATAPVALSVKNIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDD 62
           A A  AL ++N+HK +GD  VLKGISL A  GDVISILG+SGSGKSTFLRC+NLLE P +
Sbjct: 2   AEAIPALEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHE 61

Query: 63  GSVSLAGEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMR 122
           G + +AGE+LK+KR   G L  +D +Q++R+RS+LG VFQNFNLW HMT+L+N+IE P R
Sbjct: 62  GEILVAGEQLKLKRDKQGDLVAADGKQLNRIRSELGFVFQNFNLWPHMTILDNIIEAPRR 121

Query: 123 VQKRSRAESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPT 182
           V  +S+AE+ E AEALLAKVG+A+KR  YP  LSGGQQQR AIAR LAM PKV+LFDEPT
Sbjct: 122 VLGQSKAEATEVAEALLAKVGIADKRHVYPNQLSGGQQQRAAIARTLAMQPKVILFDEPT 181

Query: 183 SALDPELVGEVLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVF 242
           SALDPE+V EVL V+RSLAEEGRTML+VTHEM FA+ VS+ V+FLHQG VE  GTP++VF
Sbjct: 182 SALDPEMVQEVLAVIRSLAEEGRTMLLVTHEMNFAKQVSSEVVFLHQGLVEEQGTPEQVF 241

Query: 243 VECKSDRFRQFVSSHQ 258
              +S R +QF+SSH+
Sbjct: 242 DNPQSARCKQFMSSHR 257


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: 222
Number of extensions: 4
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: 263
Length of database: 257
Length adjustment: 24
Effective length of query: 239
Effective length of database: 233
Effective search space:    55687
Effective search space used:    55687
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: 47 (22.7 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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