GapMind for catabolism of small carbon sources

 

Alignments for a candidate for RR42_RS28305 in Bacillus altitudinis 41KF2b

Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate WP_008347408.1 BA79_RS16380 amino acid permease

Query= uniprot:A0A0C4YRF7
         (472 letters)



>NCBI__GCF_000691145.1:WP_008347408.1
          Length = 448

 Score =  444 bits (1141), Expect = e-129
 Identities = 217/448 (48%), Positives = 304/448 (67%), Gaps = 4/448 (0%)

Query: 16  EKDLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRALG 75
           +++L R L +RH+Q+IAIGG IG GLFLG+G+AI +AGP ++ +Y I G+AIFF+MRALG
Sbjct: 3   QQELKRDLSNRHVQLIAIGGTIGTGLFLGSGKAIQLAGPSIIFAYLIVGMAIFFVMRALG 62

Query: 76  ELLLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVPQ 135
           ELLL +    S    AE+++GP+A F TGW+YWF W++T MA++ AV VYV YWF D+PQ
Sbjct: 63  ELLLSKAGYQSLTDIAEDYLGPWASFVTGWTYWFCWIMTAMADVIAVGVYVQYWF-DIPQ 121

Query: 136 WIPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGV-TPLGPTA 194
           WIPA+  L +L   N + V +FGE+EFWFALIKV+TI+ +I +G+ ++  G  T  GP  
Sbjct: 122 WIPAIICLLILLGFNLLTVKLFGEMEFWFALIKVITILLLIGVGIVLLIIGFQTDAGP-V 180

Query: 195 SFSNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVWR 254
           + +NLW+HGG  P G  G +L+ Q+V+FAY GVEL+GV+A E  NP+K +P A N +  R
Sbjct: 181 TVTNLWSHGGLFPNGVTGFLLSFQMVIFAYVGVELVGVSAAETANPQKNIPSAINKIPLR 240

Query: 255 ILIFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNSGI 314
           IL FYVGA+ +++ + PW EL    SPFV  F  IG+P AA ++N VV+T+AAS+CNSG+
Sbjct: 241 ILFFYVGAIFVLLCINPWTELSASESPFVKTFGLIGIPVAAGLINFVVLTSAASACNSGM 300

Query: 315 FSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPEQVFVWVTS 374
           FST R+LY L+   Q P +FGR++   VPS A+  S  ++ +G LL+ ++PEQ F  VT+
Sbjct: 301 FSTSRILYNLSHQKQGPASFGRLNKHAVPSNALFVSTIVVSVGALLSKLIPEQAFGIVTT 360

Query: 375 ISLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLLSLD 434
           IS +  +W WSII+I HL Y+K       KA  F+ P  P+ N  V+    A+ V++   
Sbjct: 361 ISAICFIWVWSIILICHLKYKKT-RPELHKASTFKAPFTPFVNIAVLVLFAAILVIMLFA 419

Query: 435 PGTRVALYVAPVWFALLGIGYRFTKSRA 462
             TR AL + PVWF  L + Y   K R+
Sbjct: 420 DATRPALLLTPVWFGFLFLIYARKKRRS 447


Lambda     K      H
   0.328    0.142    0.445 

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: 721
Number of extensions: 35
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: 472
Length of database: 448
Length adjustment: 33
Effective length of query: 439
Effective length of database: 415
Effective search space:   182185
Effective search space used:   182185
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 (21.8 bits)
S2: 51 (24.3 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