GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Cereibacter sphaeroides ATCC 17029

Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate WP_011842387.1 RSPH17029_RS17510 amino acid ABC transporter ATP-binding protein

Query= TCDB::P73721
         (252 letters)



>NCBI__GCF_000015985.1:WP_011842387.1
          Length = 266

 Score =  248 bits (632), Expect = 1e-70
 Identities = 131/254 (51%), Positives = 177/254 (69%), Gaps = 6/254 (2%)

Query: 1   MTSPTAPLISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPI 60
           MT  T PL+   +++K+FG  +VL+GV+ ++   +V+SIIG SG GKSTFLR +N +E  
Sbjct: 1   MTDAT-PLLRLREIRKSFGTFEVLKGVSLDVAQGEVVSIIGASGSGKSTFLRSINVMEMP 59

Query: 61  SGGRLEVAGVDLSGAKIDQKH-----LRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKV 115
             G ++         K    H     L++LR  +GMVFQ +NL+PH+TVLQN++ AP  +
Sbjct: 60  QAGTMDFGDFHFDFRKGAASHPTKVQLQKLRAEIGMVFQSYNLWPHMTVLQNVIHAPMTL 119

Query: 116 LRIPMAEAKDRALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTS 175
            R P A+A + A   L ++GL  K D+YP +LSGGQ+QRVAIAR L MKP ++LFDE TS
Sbjct: 120 RRTPRAQAVEEAEALLARIGLYEKRDSYPARLSGGQQQRVAIARALAMKPRLMLFDEVTS 179

Query: 176 ALDPELVGEVLNVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFR 235
           ALDPELV EVL +M  LA +GMTM +VTHE+ FAR+VS+RV FF+QG++ E+G P+ V R
Sbjct: 180 ALDPELVHEVLVLMASLAADGMTMLLVTHEIAFARDVSSRVLFFDQGVMAEQGPPDRVLR 239

Query: 236 NPKSDRLRAFLSRI 249
           NP+S RLR FL RI
Sbjct: 240 NPESPRLRQFLHRI 253


Lambda     K      H
   0.321    0.139    0.397 

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: 201
Number of extensions: 8
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: 252
Length of database: 266
Length adjustment: 24
Effective length of query: 228
Effective length of database: 242
Effective search space:    55176
Effective search space used:    55176
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 (21.9 bits)
S2: 47 (22.7 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