GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Lutibaculum baratangense AMV1

Align High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate WP_023434296.1 N177_RS20205 branched-chain amino acid ABC transporter permease

Query= TCDB::P21627
         (307 letters)



>NCBI__GCF_000496075.1:WP_023434296.1
          Length = 312

 Score =  325 bits (833), Expect = 8e-94
 Identities = 171/310 (55%), Positives = 229/310 (73%), Gaps = 8/310 (2%)

Query: 6   HYLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGL 65
           +++QQL+NGLT+GS Y LIAIGYTMVYGIIGMINFAHG+++M+GS+IA IAI    +   
Sbjct: 3   YFVQQLINGLTLGSIYGLIAIGYTMVYGIIGMINFAHGDIFMVGSFIALIAIIAFGLTAG 62

Query: 66  DSVPLMMLAAFAASII---VTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVM 122
            S+ +++LA     +I   +TS +G+++ER+AYRPLRG  RL PLI+AIGMSI LQN V 
Sbjct: 63  SSLAVLILALILVLLIAMALTSVYGWTVERLAYRPLRGSFRLAPLITAIGMSIVLQNFVQ 122

Query: 123 LSQDSKEKAIPTLLPGNFVFGE-----SSMNGVVISYMQILIFVVTFLVMFGLTLFISRS 177
           ++Q ++ K +  L  G F   E      ++  V +S+ QILI V T ++M   TL I+++
Sbjct: 123 IAQGARVKPLQPLFSGGFTLMELEGPTGAVFRVNLSFAQILIIVTTVVLMTVFTLIIAKT 182

Query: 178 RLGRACRACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLA 237
            LGR+ RAC +D KM  LLG+N +  I+LTFV+GAALAAVA ++  + YGVI+  IGF+A
Sbjct: 183 SLGRSQRACEQDRKMAALLGVNVDRTISLTFVMGAALAAVAGLMYLLYYGVIDFYIGFIA 242

Query: 238 GIKAFTAAVLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTG 297
           G+KAFTAAVLGGIGS+PGAMLGGLL+G+ E F +  F  +YKDV AF +L +VL+F P+G
Sbjct: 243 GVKAFTAAVLGGIGSLPGAMLGGLLIGLIETFWSAYFSIEYKDVAAFSILAIVLIFLPSG 302

Query: 298 ILGRPEVEKV 307
           ILGRPEVEKV
Sbjct: 303 ILGRPEVEKV 312


Lambda     K      H
   0.328    0.145    0.413 

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: 358
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: 312
Length adjustment: 27
Effective length of query: 280
Effective length of database: 285
Effective search space:    79800
Effective search space used:    79800
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 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