GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livH in Desulfatiglans anilini DSM 4660

Align Branched-chain amino acid ABC transporter permease LivH; SubName: Full=Branched-chain amino acid transporter permease subunit LivH; SubName: Full=L-leucine ABC transporter membrane protein /L-isoleucine ABC transporter membrane protein /L-valine ABC transporter membrane protein (characterized, see rationale)
to candidate WP_028320915.1 H567_RS0107410 branched-chain amino acid ABC transporter permease

Query= uniprot:A0A0D9B2B6
         (307 letters)



>NCBI__GCF_000422285.1:WP_028320915.1
          Length = 291

 Score =  152 bits (385), Expect = 7e-42
 Identities = 98/294 (33%), Positives = 151/294 (51%), Gaps = 16/294 (5%)

Query: 7   FFQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGLAMMGLD 66
           F Q LV G+  G  Y LI +G +++ G++G+IN AHG++ M+  Y+ F+    L +    
Sbjct: 4   FLQTLVAGILKGGLYGLIGMGMSLIMGVMGIINLAHGQLMMVAMYITFVCFTYLGLDPYA 63

Query: 67  SVPLLMTAAFIASIVVTSSYGYSIERIAYRPLRGSNRLIP---LISAIGMSIFLQNTVLL 123
           ++ + M A F+         G  I+R A  PL     L+P   ++  +G+ + L      
Sbjct: 64  ALLITMPALFLL--------GALIQRYALNPLMEVESLLPENQVLMTVGIGMVLTEIARF 115

Query: 124 SQDSKDKSIPNLIPGNFAIGPGGAHEVLISYMQIVVFVVTLVAMLGLTLFISRSRLGRAC 183
              S  KS+      +     G +  V ++      F + L+    +  F+ ++ LGRA 
Sbjct: 116 IFSSDYKSVQTAYSSSSFFLRGISFSVALT----AAFFIALLFTGFMFWFLLKTDLGRAI 171

Query: 184 RACAEDIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVINPNAGFLVGLKAFT 243
           RA A+D   A L+G++   I  LTF IG+AL A A  LL   Y +  P+ G     KAF 
Sbjct: 172 RATAQDKDAALLMGVDAKRITILTFGIGSALVAAAGTLLMPIYYLF-PDIGSPFTRKAFV 230

Query: 244 AAVLGGIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTG 297
             +LGG+GS  GA+ GGL LG+AEAFGA   G  + D++   + +LVLLF P+G
Sbjct: 231 ITILGGLGSTVGAIFGGLTLGLAEAFGATYIGMAFDDMIGLLIFILVLLFLPSG 284


Lambda     K      H
   0.327    0.144    0.411 

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: 21
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: 307
Length of database: 291
Length adjustment: 27
Effective length of query: 280
Effective length of database: 264
Effective search space:    73920
Effective search space used:    73920
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