GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natH in Collimonas arenae Ter10

Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate WP_061531811.1 CAter10_RS00190 amino acid ABC transporter permease

Query= TCDB::Q8YPM7
         (381 letters)



>NCBI__GCF_001584165.1:WP_061531811.1
          Length = 218

 Score =  118 bits (296), Expect = 1e-31
 Identities = 70/203 (34%), Positives = 116/203 (57%), Gaps = 6/203 (2%)

Query: 174 LWNGLLLTLLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIVRGVPLIGILFLA 233
           L  G ++T+ +   S++LS  +G+LLAL + S L  V WF+  +I I+RG+P+I  LF  
Sbjct: 13  LLRGAVVTVEVTFYSLILSTVLGLLLALMKLSQLRPVSWFAASFINIIRGLPIIVQLFYI 72

Query: 234 QVMLPLFFAADVRLDRVLRAIAGLVLFSAAYMAENVRGGLQAVSRGQVEAAKALGLNTFF 293
             +LP      ++L      + GL +  + Y AEN R G++AV  GQ+EAA+++G+    
Sbjct: 73  YFVLP---ELGIQLSAFQAGVIGLGIAYSVYQAENFRAGIEAVDPGQIEAAQSIGMRRAM 129

Query: 294 VVLLIVLPQALRAVIPALVGQFIGLFKDTSLLSLVGLVELTGIARSILAQPQFIGRYAEV 353
           ++  +VLPQA R  +P      + + KD+SL+S + ++E+T  A  ++A   F  +   V
Sbjct: 130 IMRRVVLPQAFRIALPPYGNTLVMMLKDSSLVSTITVLEMTR-AGQMIASSTF--QNMTV 186

Query: 354 YLFIGLIYWLFCYSMSLASRRLE 376
           Y  + L+Y L    + L +RRLE
Sbjct: 187 YTMVALMYLLLSLPLVLLTRRLE 209


Lambda     K      H
   0.332    0.145    0.452 

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: 207
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: 381
Length of database: 218
Length adjustment: 26
Effective length of query: 355
Effective length of database: 192
Effective search space:    68160
Effective search space used:    68160
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 47 (22.7 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