GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00885 in Lutibaculum baratangense AMV1

Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate WP_023434296.1 N177_RS20205 branched-chain amino acid ABC transporter permease

Query= uniprot:D8IUY4
         (309 letters)



>NCBI__GCF_000496075.1:WP_023434296.1
          Length = 312

 Score =  243 bits (620), Expect = 4e-69
 Identities = 140/324 (43%), Positives = 198/324 (61%), Gaps = 41/324 (12%)

Query: 1   MDIFIQQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDILMVGAMVGLSLLKVVQQV 60
           M+ F+QQ+INGL LGS+Y LIA+GYTMVYG++ +INFAHGDI MVG+ + L  +     +
Sbjct: 1   MEYFVQQLINGLTLGSIYGLIAIGYTMVYGIIGMINFAHGDIFMVGSFIALIAI-----I 55

Query: 61  APGLPGIVQLVIAIVGAIPVCIVVSLL-------IERIAYRPLRNAPRLAPLITAIGVSI 113
           A GL     L + I+  I V ++   L       +ER+AYRPLR + RLAPLITAIG+SI
Sbjct: 56  AFGLTAGSSLAVLILALILVLLIAMALTSVYGWTVERLAYRPLRGSFRLAPLITAIGMSI 115

Query: 114 LLQTLAMMIWGRSPLPFPQVMPSDPVHIAG----ALISPT-----------QIMLLALAV 158
           +LQ    +  G       +V P  P+   G     L  PT           QI+++   V
Sbjct: 116 VLQNFVQIAQGA------RVKPLQPLFSGGFTLMELEGPTGAVFRVNLSFAQILIIVTTV 169

Query: 159 LAMVGLVLIVEKTKMGRAMRATAENPRIAGLMGVDANKVIVVTFAIGAGLAAIAGVMWAA 218
           + M    LI+ KT +GR+ RA  ++ ++A L+GV+ ++ I +TF +GA LAA+AG+M+  
Sbjct: 170 VLMTVFTLIIAKTSLGRSQRACEQDRKMAALLGVNVDRTISLTFVMGAALAAVAGLMYLL 229

Query: 219 NYSTAQFAMGFVPGLKAFSAAVLGGIGNIYGAMLGGILLGLIESLGAGYIGDLTGNFLGS 278
            Y    F +GF+ G+KAF+AAVLGGIG++ GAMLGG+L+GLIE+  + Y           
Sbjct: 230 YYGVIDFYIGFIAGVKAFTAAVLGGIGSLPGAMLGGLLIGLIETFWSAY--------FSI 281

Query: 279 NYQDIFAFIVLIIVLTLRPSGIMG 302
            Y+D+ AF +L IVL   PSGI+G
Sbjct: 282 EYKDVAAFSILAIVLIFLPSGILG 305


Lambda     K      H
   0.328    0.144    0.416 

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: 306
Number of extensions: 17
Number of successful extensions: 4
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: 309
Length of database: 312
Length adjustment: 27
Effective length of query: 282
Effective length of database: 285
Effective search space:    80370
Effective search space used:    80370
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