GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03040 in Collimonas arenae Ter10

Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate WP_061533333.1 CAter10_RS10285 amino acid ABC transporter ATP-binding protein

Query= reanno::pseudo3_N2E3:AO353_03040
         (254 letters)



>NCBI__GCF_001584165.1:WP_061533333.1
          Length = 240

 Score =  245 bits (626), Expect = 5e-70
 Identities = 129/247 (52%), Positives = 174/247 (70%), Gaps = 13/247 (5%)

Query: 4   LEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLN 63
           + V+ L K +G   +L+G+       +V+ +IG SGSGKSTFLRC+N LE+   G+IL++
Sbjct: 2   IHVKQLQKNFGRAHILRGIDCDIEESEVVCVIGPSGSGKSTFLRCLNGLEEASGGEILVD 61

Query: 64  NEELKLVANKDGALKAADPK-QLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMS 122
                        +K  DP   L  MR+ + MVFQ FNL+ HM+ ++N++ AP+ V  MS
Sbjct: 62  G------------IKVNDPHIDLNAMRAGVGMVFQRFNLFPHMSVLDNLIMAPMQVKKMS 109

Query: 123 KAEAREKAELYLAKVGVSHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDP 182
           KA+A   AE  L KVG+  + DA+P  +SGG+QQRVAIARALAMEP+VMLFDEPTSALDP
Sbjct: 110 KAQAVLVAEKLLQKVGLLDKIDAFPNQLSGGQQQRVAIARALAMEPKVMLFDEPTSALDP 169

Query: 183 ELVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQS 242
           ELVG+VL VM+ALA+EG TMVVVTHEM FAREV++++ F+ +GV+ E G P +VL +P +
Sbjct: 170 ELVGEVLAVMKALAEEGMTMVVVTHEMAFAREVADRVFFIDQGVIMEQGPPEQVLGSPHN 229

Query: 243 ERLQQFL 249
           ER + FL
Sbjct: 230 ERTRDFL 236


Lambda     K      H
   0.317    0.131    0.364 

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: 195
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: 254
Length of database: 240
Length adjustment: 24
Effective length of query: 230
Effective length of database: 216
Effective search space:    49680
Effective search space used:    49680
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 (21.7 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 24 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