GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Bacillus altitudinis 41KF2b

Align High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate WP_007501456.1 BA79_RS06410 amino acid ABC transporter ATP-binding protein

Query= TCDB::P21630
         (233 letters)



>NCBI__GCF_000691145.1:WP_007501456.1
          Length = 242

 Score =  120 bits (301), Expect = 2e-32
 Identities = 71/236 (30%), Positives = 132/236 (55%), Gaps = 7/236 (2%)

Query: 1   MLSFDKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRY 60
           M++F++V+ +YG+   L D+++ ++KGE+V +IG +G+GKST+L  +        G +  
Sbjct: 1   MITFEEVNKHYGQFHVLKDINLHIQKGEVVVIIGPSGSGKSTMLRCINRLESIDEGKVLV 60

Query: 61  EGEELVGLPSSTI--MRKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKDDYQVQMDKVLE 118
             +  V  P + I  +R++I +V +   ++   TV EN+ +      K   + +  +  E
Sbjct: 61  N-QVSVQHPKTNINLIRQNIGMVFQHFHLYPHKTVLENIMLAPMKVKKVSKE-EAKETAE 118

Query: 119 LFPR---LKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEI 175
            +     + E+ +     +SGG+QQ +AI R L  KP+++L DEP+  L P +I ++ ++
Sbjct: 119 FYLNKVGIPEKADTYPSRLSGGQQQRVAIARGLAMKPEVMLFDEPTSALDPEMIGEVLDV 178

Query: 176 IEQLRREGVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYL 231
           ++QL REG+T+ +V      A ++ADR   ++ GRI+   T AA    P+ + A L
Sbjct: 179 MKQLAREGMTMVVVTHEMGFAREVADRIVFIDEGRILEESTPAAFYEKPREKRAQL 234


Lambda     K      H
   0.318    0.136    0.374 

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: 114
Number of extensions: 4
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: 233
Length of database: 242
Length adjustment: 23
Effective length of query: 210
Effective length of database: 219
Effective search space:    45990
Effective search space used:    45990
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 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