GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Sphingomonas koreensis DSMZ 15582

Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate Ga0059261_0201 Ga0059261_0201 Na+/H+-dicarboxylate symporters

Query= TCDB::Q848I3
         (444 letters)



>FitnessBrowser__Korea:Ga0059261_0201
          Length = 455

 Score =  273 bits (697), Expect = 1e-77
 Identities = 146/364 (40%), Positives = 224/364 (61%), Gaps = 11/364 (3%)

Query: 43  FIKLIKMVIAPIIFCTVVSGIAGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQ 102
           F++LIKM+IAP++F T+V+GIA M +  ++G+ GG A+ +F   S ++L +GL++VN+ Q
Sbjct: 56  FLRLIKMIIAPLVFATLVAGIAHMGDTAALGRVGGRAVAWFICASLVSLTLGLILVNLFQ 115

Query: 103 PGNGMHIDVSTLDASKVAAYVTAGKDQS---IVGFILNVIPNTIVGAFANGDILQVLMFS 159
           PG G++  +  +DA       T+G +++   +  F  +V P + + A A  +ILQ+++FS
Sbjct: 116 PGVGLNFPLPPVDA-------TSGVEKAAFNLKDFFTHVFPASGIEAMAKNEILQIVIFS 168

Query: 160 VIFGFALHRLGAYGKPVLDFIDRFAHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLV 219
           +  G A+  +G   KP++  ++   HVM  + N +M+ API    A+A T+   G   + 
Sbjct: 169 LFIGVAITAVGEKAKPLVSAVEALVHVMLQVTNYVMRFAPIAVFAAVAGTLAERGPAIIG 228

Query: 220 QLGQLMICFYITCVLFVLVVLGAICRAHGFSVLKLIRYIREELLIVLGTSSSESALPRML 279
            L   M  FYI       +++G      G     L+RYIR+ LL+   T+SSE+A PR L
Sbjct: 229 NLAYFMGTFYIAMFTLWALLIGVCYLIVGKRTGLLVRYIRDPLLLAFSTASSEAAYPRTL 288

Query: 280 IKMERLGAKKSVVGLVIPTGYSFNLDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLL 339
             ++R G    +   V+P GYSFNLDG+ IY+T A +FIAQA    + +  +IT+LLVL+
Sbjct: 289 EALDRFGVPPRIASFVLPLGYSFNLDGSMIYMTFATIFIAQAYGIDLTLGQEITMLLVLM 348

Query: 340 LSSKGAAGVTGSGFIVLAATLSAVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATVV 399
           ++SKG AGV  +  +V+AATL     +P AGL LILGID F+   R+ TN+VGNAVA+ V
Sbjct: 349 ITSKGIAGVPRASLVVIAATLGFF-DIPEAGLLLILGIDHFLDMGRSATNVVGNAVASAV 407

Query: 400 VAKW 403
           VAKW
Sbjct: 408 VAKW 411


Lambda     K      H
   0.326    0.142    0.402 

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: 519
Number of extensions: 29
Number of successful extensions: 3
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: 444
Length of database: 455
Length adjustment: 33
Effective length of query: 411
Effective length of database: 422
Effective search space:   173442
Effective search space used:   173442
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 (21.6 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