GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dlsT in Shewanella sp. ANA-3

Align Serine transporter (characterized)
to candidate 7025821 Shewana3_2970 HAAAP family transport protein (RefSeq)

Query= SwissProt::Q8XAF5
         (443 letters)



>FitnessBrowser__ANA3:7025821
          Length = 423

 Score =  650 bits (1676), Expect = 0.0
 Identities = 326/424 (76%), Positives = 376/424 (88%), Gaps = 3/424 (0%)

Query: 20  AGMSESEWREAIKFDSTDTGWVIMSIGMAIGAGIVFLPVQVGLMGLWVFLLSSVIGYPAM 79
           A ++ ++W+E  +FDSTD GW+IMSIGMAIGAGIVFLPVQVGLMGLWVFLLSSVIGYPAM
Sbjct: 3   ARLTAAQWKEDTRFDSTDWGWIIMSIGMAIGAGIVFLPVQVGLMGLWVFLLSSVIGYPAM 62

Query: 80  YLFQRLFINTLAESPECKDYPSVISGYLGKNWGILLGALYFVMLVIWMFVYSTAITNDSA 139
           YLFQRLFINTLAESPECKDYPSVISGYLGKNWGILLG LYF+MLVIW+FVYSTAITNDSA
Sbjct: 63  YLFQRLFINTLAESPECKDYPSVISGYLGKNWGILLGGLYFIMLVIWVFVYSTAITNDSA 122

Query: 140 SYLHTFGVTEGLLSDSPFYGLVLICILVAISSRGEKLLFKISTGMVLTKLLVVAALGVSM 199
           S+L +FG T  LLS++PFYGL LIC LVA++SRGE LLFKIST MVLTKL VVA LG+ M
Sbjct: 123 SFLQSFGATTSLLSENPFYGLALICGLVALASRGENLLFKISTFMVLTKLGVVAVLGLMM 182

Query: 200 VGMWHLYNVGSLPPLGLLVKNAIITLPFTLTSILFIQTLSPMVISYRSREKSIEVARHKA 259
           V  W + N+GS+P  G  +K+AI+ LPFTLTSILFIQ+LSPMVISYRSREKS+ VAR KA
Sbjct: 183 VDKWDINNIGSVPSTGDWLKDAIVMLPFTLTSILFIQSLSPMVISYRSREKSLAVARFKA 242

Query: 260 LRAMNIAFGILFIIVFFYAVSFTLAMGHDEAVKAYEQNISALAIAAQFISGDGAAWVKVV 319
           +RAMNIAFG+LF++VFFYAVSFTLAMGH++AV+A  +NISALA+ AQ + G     +K++
Sbjct: 243 MRAMNIAFGVLFVVVFFYAVSFTLAMGHEQAVRASHENISALAMVAQGMPGQ---TLKLL 299

Query: 320 SVILNIFAVMTAFFGVYLGFREATQGIVMNILRRKMPAEKINENLVQRGIMIFAILLAWS 379
           S+ LNIFAVMTA+FGVYLGFREA QG+ MN+LRR MP E+IN++LV  GIMIF ILL+W 
Sbjct: 300 SLTLNIFAVMTAYFGVYLGFREACQGLTMNMLRRVMPEERINKSLVGYGIMIFTILLSWG 359

Query: 380 AIVLNAPVLSFTSICSPIFGLVGCLIPAWLVYKVPALHKYKGMSLYLIIVTGLLLCVSPF 439
           AIVLNAPVLSFTSICSPIFGLVGCLIPA+LVY+VPALHKYKG+SLY+IIVTGLLLC+SP 
Sbjct: 360 AIVLNAPVLSFTSICSPIFGLVGCLIPAYLVYQVPALHKYKGVSLYIIIVTGLLLCISPL 419

Query: 440 LAFS 443
           LAFS
Sbjct: 420 LAFS 423


Lambda     K      H
   0.328    0.141    0.424 

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: 716
Number of extensions: 21
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: 443
Length of database: 423
Length adjustment: 32
Effective length of query: 411
Effective length of database: 391
Effective search space:   160701
Effective search space used:   160701
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 (21.7 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