GapMind for catabolism of small carbon sources

 

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

Align Probable inositol transporter 2 (characterized)
to candidate Echvi_2805 Echvi_2805 MFS transporter, sugar porter (SP) family

Query= SwissProt::Q9C757
         (580 letters)



>FitnessBrowser__Cola:Echvi_2805
          Length = 448

 Score =  210 bits (535), Expect = 9e-59
 Identities = 128/341 (37%), Positives = 199/341 (58%), Gaps = 19/341 (5%)

Query: 27  YVLRLAFSAGIGGLLFGYDTGVISGALLYIRDDFKSVDRNTWLQEMIVSMAVAGAIVGAA 86
           YV+ L+  A +GG LFG+DT VISGA  +I++ ++  D   W   M V++A+ G ++GA 
Sbjct: 6   YVIFLSIVAALGGFLFGFDTAVISGAERFIQEKWQLSD---WTHGMAVAIALYGTVIGAL 62

Query: 87  IGGWANDKLGRRSAILMADFLFLLGAIIMAAAPNPSLLVVGRVFVGLGVGMASMTAPLYI 146
            GG   DK GR++++L    L+ + A+  A AP+    +  R   GLGVG +S+ AP+YI
Sbjct: 63  FGGIPADKYGRKTSLLWIGVLYFISALGSALAPDVYSFMFFRFIGGLGVGASSVVAPMYI 122

Query: 147 SEASPAKIRGALVSTNGFLITGGQFLSYLIN--LAFTDVTGTWRWMLGIAGIPALLQFVL 204
           SE +PAK RG LV+   F I  G  ++Y  N  +   D+  +WRWM+G+  IPAL+  +L
Sbjct: 123 SEIAPAKNRGVLVALYQFNIVFGILMAYFSNYLIEMADLNESWRWMMGMEAIPALIYTLL 182

Query: 205 MFTLPESPRWLY-RKGREEEAKAILRRIYSAEDVEQEIRALKDSVETEILEEGSSEKINM 263
              +P+SPRWL     + EEA  ILR+    E V++ I           +EE + EKI +
Sbjct: 183 SIRVPKSPRWLIAHHNKVEEATQILRKT-DPEGVDEAIHL--------AIEERNREKIKV 233

Query: 264 --IKLCKAKTVRRGLIAGVGLQVFQQFVGINTVMYYSPTIVQLAGFASNRTALLLSLVTA 321
               L K   ++  L+A + + +F Q  GIN ++Y++P + ++AG    ++ALL ++   
Sbjct: 234 GFAVLFKHSHLKTTLLA-IMIALFNQLSGINAIIYFAPRVFEMAGI-DQKSALLSTIGIG 291

Query: 322 GLNAFGSIISIYFIDRIGRKKLLIISLFGVIISLGILTGVF 362
            +N   ++I +Y IDRIGRKKL++I   G IISL ++   F
Sbjct: 292 VVNMIATMIGLYLIDRIGRKKLMVIGSIGYIISLLLMAYSF 332



 Score = 58.5 bits (140), Expect = 5e-13
 Identities = 33/107 (30%), Positives = 56/107 (52%), Gaps = 1/107 (0%)

Query: 451 NFGWFALLGLGLYIIFFSPGMGTVPWIVNSEIYPLRFRGICGGIAATANWISNLIVAQSF 510
           N G+  L  + ++I   + G G+V W+  SE++P   R     I    +WI   ++A  F
Sbjct: 338 NSGYLPLF-VFVFIASHAVGQGSVIWVFISEVFPNETRAFGQSIGCFTHWILAAVIANVF 396

Query: 511 LSLTEAIGTSWTFLIFGVISVIALLFVMVCVPETKGMPMEEIEKMLE 557
                + G +  F  F V+  + LL+V+  +PETKG  +EEI++ L+
Sbjct: 397 PFFANSFGPASIFGFFAVMMGLQLLWVLTKMPETKGRSLEEIQQDLK 443


Lambda     K      H
   0.324    0.139    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: 665
Number of extensions: 43
Number of successful extensions: 7
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: 580
Length of database: 448
Length adjustment: 34
Effective length of query: 546
Effective length of database: 414
Effective search space:   226044
Effective search space used:   226044
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 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