GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cycA in Bacillus altitudinis 41KF2b

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

Query= SwissProt::P0AAE0
         (470 letters)



>NCBI__GCF_000691145.1:WP_008347408.1
          Length = 448

 Score =  482 bits (1241), Expect = e-141
 Identities = 228/446 (51%), Positives = 324/446 (72%), Gaps = 9/446 (2%)

Query: 15  AEQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAM 74
           A+Q L+R+L+NRH+QLIAIGG IGTGLF+GSGK I LAGPSIIF Y+I+G  +FFVMRA+
Sbjct: 2   AQQELKRDLSNRHVQLIAIGGTIGTGLFLGSGKAIQLAGPSIIFAYLIVGMAIFFVMRAL 61

Query: 75  GELLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPDLS 134
           GELLLS   Y+S +D A D LGPWA + TGWTYWFCW++T MADV+A+  Y Q+WF D+ 
Sbjct: 62  GELLLSKAGYQSLTDIAEDYLGPWASFVTGWTYWFCWIMTAMADVIAVGVYVQYWF-DIP 120

Query: 135 DWVASLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPTGVE 194
            W+ ++  +++LL  NL TVK+FGEMEFWFA+IK++ I+ LI VG+V++ + FQ+  G  
Sbjct: 121 QWIPAIICLLILLGFNLLTVKLFGEMEFWFALIKVITILLLIGVGIVLLIIGFQTDAG-P 179

Query: 195 ASFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSIPI 254
            +  +LW+ GG FP G++GF   FQ+ +FA+VG+ELVG +AAET +P+K++P AIN IP+
Sbjct: 180 VTVTNLWSHGGLFPNGVTGFLLSFQMVIFAYVGVELVGVSAAETANPQKNIPSAINKIPL 239

Query: 255 RIIMFYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSANSG 314
           RI+ FYV A+ V++ + PW+ +   +SPFV+ F L+G+P AA +INFVVLTSAAS+ NSG
Sbjct: 240 RILFFYVGAIFVLLCINPWTELSASESPFVKTFGLIGIPVAAGLINFVVLTSAASACNSG 299

Query: 315 VFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIGAFTM 374
           +FSTSR+L+ L+ +   P +F +L+K AVP+  L  S I +  G ++  + P    AF +
Sbjct: 300 MFSTSRILYNLSHQKQGPASFGRLNKHAVPSNALFVSTIVVSVGALLSKLIPE--QAFGI 357

Query: 375 ITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCWVCMAFFVFVVVLLT 434
           +TT+SAI F++VW+IIL  +L Y+K RP LH+ S +K P    +    +  F  ++V++ 
Sbjct: 358 VTTISAICFIWVWSIILICHLKYKKTRPELHKASTFKAPFTPFVNIAVLVLFAAILVIML 417

Query: 435 LEDDTRQALLVTPLWFIALGLGWLFI 460
             D TR ALL+TP+WF     G+LF+
Sbjct: 418 FADATRPALLLTPVWF-----GFLFL 438


Lambda     K      H
   0.329    0.141    0.440 

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: 696
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: 470
Length of database: 448
Length adjustment: 33
Effective length of query: 437
Effective length of database: 415
Effective search space:   181355
Effective search space used:   181355
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