GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cycA in Frischella perrara PEB0191

Align D-serine/D-alanine/glycine transporter (characterized)
to candidate WP_039103492.1 FPB0191_RS01500 D-serine/D-alanine/glycine transporter

Query= SwissProt::P0AAE0
         (470 letters)



>NCBI__GCF_000807275.1:WP_039103492.1
          Length = 467

 Score =  658 bits (1697), Expect = 0.0
 Identities = 313/443 (70%), Positives = 380/443 (85%), Gaps = 1/443 (0%)

Query: 16  EQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMG 75
           E+ L+RNL+NRHIQLIAI GAIGTGLFMGSGKTISLAGPSIIFVYMIIGF+LFFVMRAMG
Sbjct: 12  EKKLKRNLSNRHIQLIAISGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFILFFVMRAMG 71

Query: 76  ELLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPDLSD 135
           E+LLSNL YKSFSDFA+DLLGPWAG+FTGWTYWFCWV+TG+ADVVAI  YAQ WFP L  
Sbjct: 72  EILLSNLNYKSFSDFAADLLGPWAGFFTGWTYWFCWVITGIADVVAIAGYAQHWFPTLEA 131

Query: 136 WVASLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSP-TGVE 194
           W+  L  I +LL+LNL TVKMFGE EFWF+MIKI+AI++LIVVG++++   + S  T   
Sbjct: 132 WIPMLICIFVLLSLNLLTVKMFGETEFWFSMIKIIAILALIVVGIILLLTSYHSEQTNTS 191

Query: 195 ASFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSIPI 254
           A+ ++LW  GG FP G+ GFFAGFQIA+FAFVGIELVGTTAAET+DP K+LPRAINS+P+
Sbjct: 192 AALSNLWQYGGLFPNGMMGFFAGFQIAIFAFVGIELVGTTAAETQDPTKNLPRAINSVPL 251

Query: 255 RIIMFYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSANSG 314
           RII FYVFALI+IM+VTPW  +   KSPFVELF L+GLPAAAS+INFVVLTSAASSANSG
Sbjct: 252 RIIFFYVFALIIIMTVTPWVFISANKSPFVELFTLIGLPAAASLINFVVLTSAASSANSG 311

Query: 315 VFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIGAFTM 374
           ++STSRMLFGLA++  AP  F +LS+R VPA GL FSC+CLL GVV++Y+ P V+ AFT+
Sbjct: 312 IYSTSRMLFGLARKNDAPSIFGRLSRRFVPANGLMFSCLCLLSGVVLIYLVPDVMTAFTI 371

Query: 375 ITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCWVCMAFFVFVVVLLT 434
           +TT+SAILFMF+W+IIL SY+ YRK+R  LH++S++KMP G +MC++C+AFF FV+VLLT
Sbjct: 372 VTTISAILFMFIWSIILLSYIQYRKKRQQLHQQSLFKMPGGIMMCFICLAFFAFVIVLLT 431

Query: 435 LEDDTRQALLVTPLWFIALGLGW 457
            E+DTRQALL TP+WF+ L + +
Sbjct: 432 FENDTRQALLATPIWFLILAISY 454


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: 779
Number of extensions: 23
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: 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 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