GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5405 in Stutzerimonas stutzeri A1501

Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate WP_011911265.1 PST_RS00075 ectoine/hydroxyectoine ABC transporter ATP-binding protein EhuA

Query= reanno::pseudo6_N2E2:Pf6N2E2_5405
         (254 letters)



>NCBI__GCF_000013785.1:WP_011911265.1
          Length = 279

 Score =  226 bits (577), Expect = 3e-64
 Identities = 126/261 (48%), Positives = 167/261 (63%), Gaps = 14/261 (5%)

Query: 4   AIKQPVSPEGIIQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRL 63
           A   P  P  +++   V K YG+  VL+ ++L+V++GE++ + GPSGSGKST +R L  L
Sbjct: 17  AAAAPAQP--MVRFASVTKRYGELTVLEGLDLDVQEGEKVAIIGPSGSGKSTLLRVLMTL 74

Query: 64  EEHQQGRIVVDGVELTN-----------DLKQIEAIRREVGMVFQHFNLFPHLTILQNCT 112
           E    G I VDG  LT+           + + +  +R +VGMVFQ FNLFPH+  LQN  
Sbjct: 75  EGIDDGLIEVDGEPLTHMPDGHGRLVPANARHLRRVRGKVGMVFQSFNLFPHMNALQNVM 134

Query: 113 LAPMWVRKMPKRKAEEIAMHYLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIML 172
            AP+ V  + KR+A E A   L  V + ++   +P QLSGGQQQRVAIARAL M+PK+ML
Sbjct: 135 EAPVQVLGLSKREARERAEELLAMVGLEDKLEHFPAQLSGGQQQRVAIARALAMRPKVML 194

Query: 173 FDEPTSALDPEMVKEVLDTMIGLAE-DGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQA 231
           FDE TSALDPE+  EVL  +  L E   +TML VTH+MGFAR  A+RV F  +G I EQ 
Sbjct: 195 FDEVTSALDPELCGEVLSVIRRLGEAHNLTMLMVTHQMGFAREFADRVCFFHQGRIHEQG 254

Query: 232 APNDFFDNPQNDRTKLFLSQI 252
           +P+  F+NPQ DRT+ FLS +
Sbjct: 255 SPDALFNNPQEDRTREFLSAV 275


Lambda     K      H
   0.322    0.137    0.407 

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: 212
Number of extensions: 6
Number of successful extensions: 3
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: 254
Length of database: 279
Length adjustment: 25
Effective length of query: 229
Effective length of database: 254
Effective search space:    58166
Effective search space used:    58166
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 (21.9 bits)
S2: 47 (22.7 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