GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livH in Azospirillum brasilense Sp245

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 AZOBR_RS08235 AZOBR_RS08235 branched-chain amino acid transporter permease subunit LivH

Query= uniprot:A0A0D9B2B6
         (307 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS08235 AZOBR_RS08235
           branched-chain amino acid transporter permease subunit
           LivH
          Length = 301

 Score =  350 bits (899), Expect = e-101
 Identities = 173/302 (57%), Positives = 231/302 (76%), Gaps = 3/302 (0%)

Query: 6   HFFQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGLAMMGL 65
           +F QQL+NGL++G+ Y LIAIGYTMVYGIIGMINFAHGE+YMIG++VA I    +  +G+
Sbjct: 3   YFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGI 62

Query: 66  DSVPLLMTAAFIASIVVTSSYGYSIERIAYRPLRGSNRLIPLISAIGMSIFLQNTVLLSQ 125
             VPL +    +AS++ T+ YG+++ERIAYRPLR S RL PLISAIGMSIFLQN V + Q
Sbjct: 63  TWVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQILQ 122

Query: 126 DSKDKSIPNLIPGNFAIGPGGAHEVLISYMQIVVFVVTLVAMLGLTLFISRSRLGRACRA 185
            ++ K +  ++PGN  +  G    V +SY+++   V+T+  M G T  I+R+ LGRA RA
Sbjct: 123 GARSKPLQPILPGNLTLMDGA---VSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRA 179

Query: 186 CAEDIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVINPNAGFLVGLKAFTAA 245
           C +D KMA LLG+N + +I+LTFV+GAALAA+A +++ + YGVI+   GFL G+KAFTAA
Sbjct: 180 CEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAA 239

Query: 246 VLGGIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTGILGRPEVE 305
           VLGGIGS+PGAMLGG+V+G+ EAF +   G ++KDV  F +LVLVL+FRPTG+LGRPE+E
Sbjct: 240 VLGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGRPEIE 299

Query: 306 KV 307
           KV
Sbjct: 300 KV 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: 353
Number of extensions: 11
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: 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, the preprint on GapMind for carbon sources, 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