GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cycA in Pantoea rwandensis LMG 26275

Align D-serine/D-alanine/glycine transporter (characterized)
to candidate WP_084934657.1 HA51_RS11575 D-serine/D-alanine/glycine transporter

Query= SwissProt::A0A0H2VDI7
         (470 letters)



>NCBI__GCF_002095475.1:WP_084934657.1
          Length = 463

 Score =  723 bits (1867), Expect = 0.0
 Identities = 354/463 (76%), Positives = 402/463 (86%), Gaps = 1/463 (0%)

Query: 1   MVDQVKVVADDQAPAEQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVY 60
           MVDQ K  A  +A   + LRRNL NRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVY
Sbjct: 1   MVDQSKE-ALIEAEQPEKLRRNLHNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVY 59

Query: 61  MIIGFMLFFVMRAMGELLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVV 120
           MIIGFMLFFVMRAMGELLLSNLEYKSFSDFA+DLLGPWAGYFTGWTYWFCWVVTG+ADVV
Sbjct: 60  MIIGFMLFFVMRAMGELLLSNLEYKSFSDFAADLLGPWAGYFTGWTYWFCWVVTGIADVV 119

Query: 121 AITAYAQFWFPGLSDWVASLSVIILLLVLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGL 180
           AI+AY Q WFPG S W+++L  I   L LN+ATVK+FGEMEFWFA+IKIVAIV+LI+ G+
Sbjct: 120 AISAYFQLWFPGFSIWMSALLCIFAFLALNIATVKLFGEMEFWFAIIKIVAIVALIITGI 179

Query: 181 VMVAMHFQSPTGVEASFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKD 240
           V+V+MH+ SP G  AS +++W+ GG FPKGLSGFFAGFQIAVFAFVGIELVGT AAETKD
Sbjct: 180 VLVSMHYPSPNGTTASLSNIWDHGGMFPKGLSGFFAGFQIAVFAFVGIELVGTAAAETKD 239

Query: 241 PEKSLPRAINSIPIRIIMFYVFSLIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVIN 300
           P K LPRAIN+IP+RIIMFYV +L+VIM+VTPW+ V+P +SPFVE+FVL+GLPAAAS++N
Sbjct: 240 PHKVLPRAINAIPVRIIMFYVLALLVIMAVTPWNQVLPNRSPFVEMFVLIGLPAAASIVN 299

Query: 301 FVVLTSAASSANSGVFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVV 360
           FVVLTSAASSANSG+FSTSRMLFGLA+ GVA KAF +LS RAVP  GL FSC+CLL GV 
Sbjct: 300 FVVLTSAASSANSGIFSTSRMLFGLAELGVAHKAFGRLSARAVPTTGLFFSCLCLLVGVA 359

Query: 361 MLYVNPSVIGAFTMITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCW 420
           ++Y+ P V+  FTM+TTVSAILFMFVWTIILCSYL YRKQ P  H  S +KMPLGK MCW
Sbjct: 360 LIYLIPDVMTVFTMVTTVSAILFMFVWTIILCSYLAYRKQHPQRHAASKFKMPLGKFMCW 419

Query: 421 VCMAFFVFVLVLLTLEDDTRQALLVTPLWFIALGLGWLFIGKK 463
           VCMAFF FVLVLLTL++DTRQAL+VTPLWF+ L LGWL   +K
Sbjct: 420 VCMAFFAFVLVLLTLQEDTRQALMVTPLWFVILTLGWLLRRRK 462


Lambda     K      H
   0.329    0.141    0.441 

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: 832
Number of extensions: 16
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: 463
Length adjustment: 33
Effective length of query: 437
Effective length of database: 430
Effective search space:   187910
Effective search space used:   187910
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