GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galP in Echinicola vietnamensis KMM 6221, DSM 17526

Align Arabinose-proton symporter; Arabinose transporter (characterized)
to candidate Echvi_2805 Echvi_2805 MFS transporter, sugar porter (SP) family

Query= SwissProt::P96710
         (464 letters)



>FitnessBrowser__Cola:Echvi_2805
          Length = 448

 Score =  298 bits (762), Expect = 3e-85
 Identities = 169/444 (38%), Positives = 257/444 (57%), Gaps = 6/444 (1%)

Query: 18  HSMGFVILISCAAGLGGLLYGYDTAVISGAIGFLKDLYSLSPFMEGLVISSIMIGGVVGV 77
           +S  +VI +S  A LGG L+G+DTAVISGA  F+++ + LS +  G+ ++  + G V+G 
Sbjct: 2   NSKKYVIFLSIVAALGGFLFGFDTAVISGAERFIQEKWQLSDWTHGMAVAIALYGTVIGA 61

Query: 78  GISGFLSDRFGRRKILMTAALLFAISAIVSALSQDVSTLIIARIIGGLGIGMGSSLSVTY 137
              G  +D++GR+  L+   +L+ ISA+ SAL+ DV + +  R IGGLG+G  S ++  Y
Sbjct: 62  LFGGIPADKYGRKTSLLWIGVLYFISALGSALAPDVYSFMFFRFIGGLGVGASSVVAPMY 121

Query: 138 ITEAAPPAIRGSLSSLYQLFTILGISATYFINLAVQRSGTYEWGVHTGWRWMLAYGMVPS 197
           I+E AP   RG L +LYQ   + GI   YF N  ++ +   E      WRWM+    +P+
Sbjct: 122 ISEIAPAKNRGVLVALYQFNIVFGILMAYFSNYLIEMADLNE-----SWRWMMGMEAIPA 176

Query: 198 VIFFLVLLVVPESPRWL-AKAGKTNEALKILTRINGETVAKEELKNIENSLKIEQMGSLS 256
           +I+ L+ + VP+SPRWL A   K  EA +IL + + E V +     IE   + +     +
Sbjct: 177 LIYTLLSIRVPKSPRWLIAHHNKVEEATQILRKTDPEGVDEAIHLAIEERNREKIKVGFA 236

Query: 257 QLFKPGLRKALVIGILLALFNQVIGMNAITYYGPEIFKMMGFGQNAGFVTTCIVGVVEVI 316
            LFK    K  ++ I++ALFNQ+ G+NAI Y+ P +F+M G  Q +  ++T  +GVV +I
Sbjct: 237 VLFKHSHLKTTLLAIMIALFNQLSGINAIIYFAPRVFEMAGIDQKSALLSTIGIGVVNMI 296

Query: 317 FTVIAVLLIDKVGRKKLMSIGSAFMAIFMILIGTSFYFELTSGIMMIVLILGFVAAFCVS 376
            T+I + LID++GRKKLM IGS    I ++L+  SF   + +   + + +  F+A+  V 
Sbjct: 297 ATMIGLYLIDRIGRKKLMVIGSIGYIISLLLMAYSFSGGVINSGYLPLFVFVFIASHAVG 356

Query: 377 VGPITWIMISEIFPNHLRARAAGIATIFLWGANWAIGQFVPMMIDSFGLAYTFWIFAVIN 436
            G + W+ ISE+FPN  RA    I     W     I    P   +SFG A  F  FAV+ 
Sbjct: 357 QGSVIWVFISEVFPNETRAFGQSIGCFTHWILAAVIANVFPFFANSFGPASIFGFFAVMM 416

Query: 437 ILCFLFVVTICPETKNKSLEEIEK 460
            L  L+V+T  PETK +SLEEI++
Sbjct: 417 GLQLLWVLTKMPETKGRSLEEIQQ 440


Lambda     K      H
   0.327    0.142    0.425 

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: 545
Number of extensions: 25
Number of successful extensions: 4
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: 464
Length of database: 448
Length adjustment: 33
Effective length of query: 431
Effective length of database: 415
Effective search space:   178865
Effective search space used:   178865
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