GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Methylocystis bryophila S285

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_085770499.1 B1812_RS04360 ABC transporter ATP-binding protein

Query= TCDB::P21630
         (233 letters)



>NCBI__GCF_002117405.1:WP_085770499.1
          Length = 266

 Score =  188 bits (477), Expect = 1e-52
 Identities = 103/236 (43%), Positives = 154/236 (65%), Gaps = 8/236 (3%)

Query: 5   DKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLL-----MTLCGSPQAASGSIR 59
           D  ++Y   I AL DVS++V++GEIV L+GANG+GK+T+L     +      Q  SG I 
Sbjct: 12  DVEASYNQAIVALRDVSLKVRRGEIVALLGANGSGKTTILNATSRLLAAERGQITSGKIL 71

Query: 60  YEGEELVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFF--TDKDDYQVQMDKVL 117
           ++G       ++ + +K +  V EGRRVF  LTVEENLA G     +++ + +  +D V 
Sbjct: 72  FDGRSTSKSSTAELAQKGLVQVLEGRRVFRSLTVEENLASGALARRSNRRELRDDLDYVY 131

Query: 118 ELFPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIE 177
            +FP+LK R    AG +SGGEQQM AIGRA+M+ P+LL+LDEPS+GLAP+++++I++++ 
Sbjct: 132 GVFPQLKHRRRSLAGLLSGGEQQMTAIGRAMMTHPRLLILDEPSMGLAPLVVEEIYQVLG 191

Query: 178 QLRR-EGVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYLG 232
            L R +G+++ + EQNA  AL+ A R YV+ENG +V+    A L     V+D YLG
Sbjct: 192 ALNRMKGLSLLVAEQNAYVALRHAHRGYVVENGVVVLEGAAATLQEREDVKDFYLG 247


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: 164
Number of extensions: 6
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: 233
Length of database: 266
Length adjustment: 24
Effective length of query: 209
Effective length of database: 242
Effective search space:    50578
Effective search space used:    50578
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 Apr 09 2024. 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