GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacK in Persephonella marina EX-H1

Align ABC transporter for Lactose, ATPase component (characterized)
to candidate WP_012676175.1 PERMA_RS01260 ATP-binding cassette domain-containing protein

Query= reanno::Smeli:SM_b20002
         (358 letters)



>NCBI__GCF_000021565.1:WP_012676175.1
          Length = 261

 Score =  137 bits (345), Expect = 3e-37
 Identities = 79/226 (34%), Positives = 126/226 (55%), Gaps = 6/226 (2%)

Query: 6   LSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLTIDDV 65
           + ++ K +G  EV+K +  D+K GE  V +G SG GKST ++ I GL + +SG + +DD 
Sbjct: 7   VQNLTKKFGEREVLKNISFDVKEGEIFVIMGGSGSGKSTTIKHIIGLLKPTSGKIIVDDT 66

Query: 66  RMNDVDPS-----KRGIAMVFQSYALYPHMTVRENMGFA-LRFAGVPRAEIEKRVNEAAH 119
            +  +        ++ +  +FQ  AL+  +TV EN+GF  L    +P  +I K   E   
Sbjct: 67  DITALSDRELIEFRKRMGYLFQEGALFDSLTVWENVGFYFLENTKMPVKDIRKIAVEKLS 126

Query: 120 ILELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARL 179
           ++ L  + D  P QLSGG R+RV++ RAI   P+I L+DEP S LD      +   I  L
Sbjct: 127 LVGLKGIEDLYPSQLSGGMRKRVSLARAISTDPEIILYDEPTSGLDPVTSAMIDNLIVHL 186

Query: 180 HKQLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDP 225
             ++  T + VTHD   A ++AD+I ++  GV+  VG+P ++ + P
Sbjct: 187 RDKIGVTSIVVTHDLDSAFSIADRIAMIHKGVIYAVGTPDEIKNHP 232


Lambda     K      H
   0.321    0.139    0.396 

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: 256
Number of extensions: 14
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: 358
Length of database: 261
Length adjustment: 27
Effective length of query: 331
Effective length of database: 234
Effective search space:    77454
Effective search space used:    77454
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 (21.8 bits)
S2: 48 (23.1 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