GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Bacillus altitudinis 41KF2b

Align High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate WP_017368436.1 BA79_RS17265 ABC transporter ATP-binding protein

Query= TCDB::P21629
         (255 letters)



>NCBI__GCF_000691145.1:WP_017368436.1
          Length = 571

 Score =  104 bits (259), Expect = 5e-27
 Identities = 75/236 (31%), Positives = 122/236 (51%), Gaps = 19/236 (8%)

Query: 21  VNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRLDGEEIQG-LPGHKIAR 79
           +N ++  V++ +++S+ G NGAGKTT+   L  F +PT G I L+G++I G     +  R
Sbjct: 319 LNNISFTVKKGEMISIAGANGAGKTTLSKVLCAFEKPTKGTIHLNGDDITGDTIKQRSER 378

Query: 80  KGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFRRSEREAMEYAAHWLE 139
            GVV    N  + K+M   E  L           L G+ +     R ER         L+
Sbjct: 379 IGVVMQNPNQMISKQMIFDEVALGL--------VLRGVKEDDIKDRVERV--------LK 422

Query: 140 EVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGLNPKETDDLKALIAKL 199
              L  F N     L++GQ++R+ IA  ++  P I++LDEP AG + +   ++   + +L
Sbjct: 423 VCGLYPFRNWPISALSFGQKKRVTIASILVLEPEIIILDEPTAGQDFRHYTEMMTFLEQL 482

Query: 200 RSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQI-RDNPDVIKAYLGE 254
            ++  VT+L+I HDM L++  +   +VI+ G  +AD TP ++  D   V KA L E
Sbjct: 483 -NQQGVTILMITHDMHLMLEYTTRTIVISDGEKIADDTPAKVLTDQLLVQKASLKE 537



 Score = 71.6 bits (174), Expect = 3e-17
 Identities = 67/260 (25%), Positives = 122/260 (46%), Gaps = 19/260 (7%)

Query: 1   MSRPILEVS--GLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPT 58
           M +P+++    G   R      +  VNL + E + V + GP+G+GK+T+ +C+ G   P 
Sbjct: 1   MKKPMIQFEHFGFKYRSQAEPTLKDVNLTIYEGEKVLIAGPSGSGKSTLAHCINGLV-PA 59

Query: 59  GGLIRLDGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLF 118
                ++G    G  G    ++ +    Q V    +    + + +     +  +    L 
Sbjct: 60  SYKGSMEGSLHIG--GKNAEKENIFSLSQLVGTVLQDPDGQFIGLT----VGEDIAFTLE 113

Query: 119 KTPAFRRSEREAMEYAAHWLEEVNLTEFANRSAGT---LAYGQQRRLEIARCMMTRPRIL 175
                R   +  +E AA       LTE   + A +   L+ GQ++R+ IA  ++    IL
Sbjct: 114 NDQVTREEMKTRVEKAA------KLTEVDGKLASSVHELSGGQKQRVAIAGVLVNDVDIL 167

Query: 176 MLDEPAAGLNPKETDDLKALIAKLRSEHNVTVLLIEHDMK-LVMSISDHIVVINQGAPLA 234
           + DEP A L+P    ++  LI +L+ E   TV+++EH ++ ++    D I+V+N G   A
Sbjct: 168 LFDEPLASLDPATGKEVIDLIDRLQKETKKTVVMVEHRLEDVLFRHVDRIIVVNDGTIAA 227

Query: 235 DGTPEQIRDNPDVIKAYLGE 254
           D TP+++  +  +  AYL E
Sbjct: 228 DMTPDELLASNVLEAAYLRE 247


Lambda     K      H
   0.320    0.137    0.391 

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: 359
Number of extensions: 19
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 255
Length of database: 571
Length adjustment: 30
Effective length of query: 225
Effective length of database: 541
Effective search space:   121725
Effective search space used:   121725
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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