GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livH in Desulfovibrio vulgaris Hildenborough

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 206138 DVU0713 branched-chain amino acid ABC transporter, permease protein

Query= uniprot:A0A0D9B2B6
         (307 letters)



>MicrobesOnline__882:206138
          Length = 301

 Score =  263 bits (673), Expect = 3e-75
 Identities = 144/303 (47%), Positives = 198/303 (65%), Gaps = 7/303 (2%)

Query: 7   FFQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGLAMMGLD 66
           F QQL NGL VG  YALIA+GYTMVYG++ +INFAHG+++ IG+Y+ F   A L + G  
Sbjct: 4   FLQQLTNGLAVGGIYALIALGYTMVYGVLKLINFAHGDLFTIGAYLGFTVFAALGLSGHV 63

Query: 67  S--VPLLMTAAFIASIVVTSSYGYSIERIAYRPLRGSNRLIPLISAIGMSIFLQNTVLLS 124
           S  V +L+    +  +V     GY +ER+AYRPLR S+RL  ++SA+G SIF QN V+L 
Sbjct: 64  SGAVAVLLVTTMVMGLVAL--IGYLLERVAYRPLRSSSRLSAVVSALGASIFFQNAVMLI 121

Query: 125 QDSKDKSIPNLIPGNFAIGPGGAHEVLISYMQIVVFVVTLVAMLGLTLFISRSRLGRACR 184
             +K +  PN I    A+   G     I  ++I++F  ++  ML L  FI R+R G A R
Sbjct: 122 YGAKFQVYPNDIRPTMAVSFFGMD---IPLVRIMMFGASVALMLLLHFFIHRTRTGTAIR 178

Query: 185 ACAEDIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVINPNAGFLVGLKAFTA 244
           A A D   A L+GI+ N +IAL F+IG AL   A V++ + YG I+   G++ GLKAFTA
Sbjct: 179 AVAIDQGAAKLMGIDVNRVIALVFMIGPALGGAAGVMVGLYYGQIDFTMGWVYGLKAFTA 238

Query: 245 AVLGGIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTGILGRPEV 304
           A+LGGIG+IPGAM+GGL+LGV EA GA      +KD +AF +L+L+L+ RPTG+LG    
Sbjct: 239 AILGGIGNIPGAMVGGLLLGVIEALGAAYISIAWKDAIAFLVLILILIIRPTGLLGERVA 298

Query: 305 EKV 307
           +K+
Sbjct: 299 DKI 301


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: 340
Number of extensions: 16
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: 301
Length adjustment: 27
Effective length of query: 280
Effective length of database: 274
Effective search space:    76720
Effective search space used:    76720
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 Sep 17 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