GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cycA in Klebsiella michiganensis M5al

Align D-serine/D-alanine/glycine transporter (characterized)
to candidate BWI76_RS02700 BWI76_RS02700 D-serine/D-alanine/glycine transporter

Query= SwissProt::P0AAE0
         (470 letters)



>FitnessBrowser__Koxy:BWI76_RS02700
          Length = 467

 Score =  870 bits (2249), Expect = 0.0
 Identities = 435/467 (93%), Positives = 450/467 (96%)

Query: 1   MVDQVKVVADDQAPAEQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVY 60
           MVDQVKVVAD+QAP EQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVY
Sbjct: 1   MVDQVKVVADEQAPTEQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVY 60

Query: 61  MIIGFMLFFVMRAMGELLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVV 120
           MIIGFMLFFVMRAMGELLLSNLEYKSFSDFA+DLLGPWAGYFTGWTYWFCWVVTGMADVV
Sbjct: 61  MIIGFMLFFVMRAMGELLLSNLEYKSFSDFAADLLGPWAGYFTGWTYWFCWVVTGMADVV 120

Query: 121 AITAYAQFWFPDLSDWVASLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGL 180
           AITAYAQFWFP LSDWVASLAVI+LLL LNLATVKMFGEMEFWFAMIKIVAIV+LIVVGL
Sbjct: 121 AITAYAQFWFPGLSDWVASLAVILLLLGLNLATVKMFGEMEFWFAMIKIVAIVALIVVGL 180

Query: 181 VMVAMHFQSPTGVEASFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKD 240
           VMV MHFQSPTGVEASFAHLWNDGGWFPKG+SGFFAGFQIAVFAFVGIELVGTTAAETKD
Sbjct: 181 VMVMMHFQSPTGVEASFAHLWNDGGWFPKGISGFFAGFQIAVFAFVGIELVGTTAAETKD 240

Query: 241 PEKSLPRAINSIPIRIIMFYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVIN 300
           PEKSLPRAINSIPIRIIMFYVFALIVIMSVTPWSSVVP KSPFVELFVLVGLPAAAS+IN
Sbjct: 241 PEKSLPRAINSIPIRIIMFYVFALIVIMSVTPWSSVVPSKSPFVELFVLVGLPAAASLIN 300

Query: 301 FVVLTSAASSANSGVFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVV 360
           FVVLTSAASSANSGVFSTSRMLFGLAQ+G APK FAKLSKRAVPAKGLTFSC+CLLGGVV
Sbjct: 301 FVVLTSAASSANSGVFSTSRMLFGLAQDGQAPKMFAKLSKRAVPAKGLTFSCMCLLGGVV 360

Query: 361 MLYVNPSVIGAFTMITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCW 420
           ML VNPSVI AFTMITTVSAILFMFVWTIILCSYLVYRK+RP LHE+S YKMPLGKLMCW
Sbjct: 361 MLMVNPSVIAAFTMITTVSAILFMFVWTIILCSYLVYRKKRPQLHEQSKYKMPLGKLMCW 420

Query: 421 VCMAFFVFVVVLLTLEDDTRQALLVTPLWFIALGLGWLFIGKKRAAE 467
           VCMAFF FV+VLLTLE DTR+AL+VTPLWF+ LG GWLF GKKR A+
Sbjct: 421 VCMAFFAFVLVLLTLEADTREALMVTPLWFVLLGAGWLFAGKKRLAK 467


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: 911
Number of extensions: 17
Number of successful extensions: 1
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: 467
Length adjustment: 33
Effective length of query: 437
Effective length of database: 434
Effective search space:   189658
Effective search space used:   189658
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 17 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