GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00885 in Desulfatiglans anilini DSM 4660

Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate WP_028321170.1 H567_RS0109125 branched-chain amino acid ABC transporter permease

Query= uniprot:D8IUY4
         (309 letters)



>NCBI__GCF_000422285.1:WP_028321170.1
          Length = 308

 Score =  262 bits (670), Expect = 7e-75
 Identities = 140/307 (45%), Positives = 199/307 (64%), Gaps = 9/307 (2%)

Query: 3   IFIQQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDILMVGAMVGLSLLKVVQQVA- 61
           I   Q+INGL +G +YALIALGYT+VYG+L +INFAHG+I M G+  G + L  + Q   
Sbjct: 9   ILCDQLINGLTIGGIYALIALGYTLVYGILFMINFAHGEIFMFGSFAGYAALTFLLQYGF 68

Query: 62  PGLPGIVQLVIAIVGAIPVCIVVSLLIERIAYRPLRNAPRLAPLITAIGVSILLQTLAMM 121
                +  ++ A + A+ V  ++  ++ERIAYRPLR A RLAPLI+AIG SI LQ + ++
Sbjct: 69  TEQRPLASILAAFLAAMVVSALLGTILERIAYRPLRRASRLAPLISAIGASIFLQNVMLI 128

Query: 122 IWGRSPLPFPQVMPSDPVHIAGALISPTQIMLLALAVLAMVGLVLIVEKTKMGRAMRATA 181
           I       +P ++      I    IS  QIM++  +   M GL + +++T+ GRAMRA A
Sbjct: 129 IIKGRMQVYPDLLHETFFEIGWFNISNFQIMIILGSFFLMAGLYIFIQRTRTGRAMRAVA 188

Query: 182 ENPRIAGLMGVDANKVIVVTFAIGAGLAAIAGVMWAANYSTAQFAMGFVPGLKAFSAAVL 241
           E+   A LMG+D N++I++TF IG+ LAA AGVM    Y+     MGF+PG+KAF+AAVL
Sbjct: 189 EDRSAAALMGIDVNRIIMITFVIGSALAAAAGVMVGMYYTQINHMMGFIPGIKAFTAAVL 248

Query: 242 GGIGNIYGAMLGGILLGLIESLGAGYIGDLTGNFLGSNYQDIFAFIVLIIVLTLRPSGIM 301
           GGIGN+ GAMLGG+ LGL E+ G          F+ + Y+D+ AF +L++VL  RP GI+
Sbjct: 249 GGIGNVPGAMLGGLFLGLAEAFGV--------LFMPAQYKDVIAFALLVLVLIFRPRGIL 300

Query: 302 GERVADR 308
           GE V+++
Sbjct: 301 GEVVSEK 307


Lambda     K      H
   0.328    0.144    0.416 

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: 268
Number of extensions: 15
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: 309
Length of database: 308
Length adjustment: 27
Effective length of query: 282
Effective length of database: 281
Effective search space:    79242
Effective search space used:    79242
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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