GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SLC1A4 in Shewanella loihica PV-4

Align neutral amino acid transporter B(0) (characterized)
to candidate 5208231 Shew_0743 sodium:dicarboxylate symporter (RefSeq)

Query= CharProtDB::CH_091706
         (553 letters)



>FitnessBrowser__PV4:5208231
          Length = 433

 Score =  223 bits (569), Expect = 9e-63
 Identities = 146/423 (34%), Positives = 221/423 (52%), Gaps = 62/423 (14%)

Query: 66  GLGLGVSAAGGADALGPARLTRFAFPGELLLRLLKMIILPLVVCSLIGGAASL-DPSALG 124
           GLGLG  A      L P         G L +  +KM+I+PLV CSLI G  S+ D + +G
Sbjct: 37  GLGLGEQAV----LLKPI--------GTLFVNTIKMLIVPLVFCSLIVGVTSMQDTAKMG 84

Query: 125 RVGAWALLFFLVTTLLASALGVGLALALKPGAAVTAITSINDSVVDPCARSAPTKEALDS 184
           R+G  +  F+L TT +A  LG+ +   ++PGA + A+TS         A S    + + S
Sbjct: 85  RIGFKSFAFYLGTTSIAITLGLAVGHIMQPGAGL-AMTS---------AESHNAVKEVPS 134

Query: 185 FLDLVRNIFPSNLVSAAFRSFATSYEPKDNSCKIPQSCIQREINSTMVQLLCEVEGMNIL 244
            ++ + NI P+N ++A                                     +    IL
Sbjct: 135 IMETLINIVPTNPIAA-------------------------------------LASGQIL 157

Query: 245 GLVVFAIVFGVALRKLGPEGELLIRFFNSFNDATMVLVSWIMWYAPVGILFLVASKIVEM 304
            ++VFA+  G+AL  +G  G+  I+ F S  +A   L   +M  AP G+  L+A    E 
Sbjct: 158 QVIVFAVALGIALVLIGDHGKPAIKVFESLAEAMYKLTDMVMKLAPYGVFGLMAWVAGEY 217

Query: 305 KDVRQLFISLGKYILCCLLGHAIHGLLVLPLIYFLFTRKNPYRFLWGIMTPLATAFGTSS 364
                + + L K IL   +G A+H +    L+     + NP +F  GI   LA A+ TSS
Sbjct: 218 G--MDMLMPLIKVILAVYIGCALHIIGFYSLVLTFVAKLNPMQFFKGISNALAVAYTTSS 275

Query: 365 SSATLPLMMKCVEEKNGVAKHISRFILPIGATVNMDGAALFQCVAAVFIAQLNGVSLDFV 424
           S+ TLP  MKC  E  G+ K IS F+LP+G T+NMDG AL+Q V A+F+AQ  G+ L +V
Sbjct: 276 SAGTLPASMKCASESLGINKKISSFVLPLGTTINMDGTALYQGVTALFVAQAFGIDLTWV 335

Query: 425 KIITILVTATASSVGAAGIPAGGVLTLAIILEAVSLPVKDISLILAVDWLVDRSCTVLNV 484
             ITI++TAT +S+G AG+P  G++ L ++L  V LP++ +++I  +D ++D + TV+NV
Sbjct: 336 DYITIILTATLASIGTAGVPGAGLVMLTLVLTTVGLPLEGVAIIAGIDRILDMARTVVNV 395

Query: 485 EGD 487
            GD
Sbjct: 396 SGD 398


Lambda     K      H
   0.323    0.138    0.406 

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: 428
Number of extensions: 21
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 553
Length of database: 433
Length adjustment: 34
Effective length of query: 519
Effective length of database: 399
Effective search space:   207081
Effective search space used:   207081
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 52 (24.6 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