GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltK in Halomonas xinjiangensis TRM 0175

Align PP1069, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate WP_043531902.1 JH15_RS15195 amino acid ABC transporter permease

Query= TCDB::Q88NY4
         (223 letters)



>NCBI__GCF_000759345.1:WP_043531902.1
          Length = 222

 Score =  118 bits (295), Expect = 1e-31
 Identities = 73/222 (32%), Positives = 123/222 (55%), Gaps = 8/222 (3%)

Query: 3   MDFSEI-IPALPALWEGMVMTLKLMVMGVIGGIVLGTILALMRLSSSKLLSNLAGAYVNY 61
           ++F E  I  LP L +G+ +TL L ++ +  G  LG +L   R+  ++L   ++ AYV  
Sbjct: 2   LEFIEFGIEWLPRLLQGVPVTLLLWIIAITLGFFLGLMLCWARVYGNRLFYWISTAYVEL 61

Query: 62  FRSIPLLLVITWFYLAVPFVLRWITGEDTPVGAFTSCVVAFMMFEAAYFCEIVRAGVQSI 121
           FR  P+L+ + + YL +P V            AFT+ V+A  +  AAY  E  R  V S+
Sbjct: 62  FRGTPMLVQMFFIYLGLPHV-------GIVFDAFTAAVIAITLNSAAYQAEYFRGSVLSV 114

Query: 122 SKGQMGAAQALGMNYAQTMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFLNS 181
            KGQ+ AA+A GM+  Q +R I+LPQA R++ P    ++II  + TS+ YT+G+V+    
Sbjct: 115 PKGQLVAARACGMSQWQAIRHIMLPQALRRVIPQWSNEAIIELKFTSIAYTIGVVEITAI 174

Query: 182 ARSNGDIIGRSHEFLIFAGVVYFLISFSASWLVKRLQKRISV 223
           A   G       +  ++AG++Y +++ + + L+  L++R  V
Sbjct: 175 ASDIGSRTFDFFQVFLWAGIIYLVLTSTVASLLGLLERRTYV 216


Lambda     K      H
   0.330    0.141    0.417 

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: 135
Number of extensions: 7
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: 223
Length of database: 222
Length adjustment: 22
Effective length of query: 201
Effective length of database: 200
Effective search space:    40200
Effective search space used:    40200
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 (21.9 bits)
S2: 45 (21.9 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