GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|MicrobesOnline__882:206138 DVU0713 branched-chain amino acid
           ABC transporter, permease protein
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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