GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Dyella japonica UNC79MFTsu3.2

Align Galactose-proton symporter; Galactose transporter (characterized)
to candidate N515DRAFT_1228 N515DRAFT_1228 MFS transporter, SP family, galactose:H+ symporter

Query= SwissProt::P0AEP1
         (464 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1228
          Length = 463

 Score =  605 bits (1559), Expect = e-177
 Identities = 302/450 (67%), Positives = 356/450 (79%), Gaps = 1/450 (0%)

Query: 12  KAMTFFVCFLAALAGLLFGLDIGVIAGALPFIADEFQITSHTQEWVVSSMMFGAAVGAVG 71
           K    + C LAALAGL+FGLDIGVI+GA  FI  EF I+ HT EW+VSSMMFGAAVGA+G
Sbjct: 14  KGTVIYTCVLAALAGLMFGLDIGVISGASQFIKAEFAISDHTIEWIVSSMMFGAAVGALG 73

Query: 72  SGWLSFKLGRKKSLMIGAILFVAGSLFSAAAPNVEVLILSRVLLGLAVGVASYTAPLYLS 131
           +GWLS  LGRK+SL++GAILFV GSL    A + E LI +RV+LGLA+G+A++TAPLYL+
Sbjct: 74  AGWLSSHLGRKRSLILGAILFVIGSLLCGLAWSPETLIAARVILGLAIGIATFTAPLYLA 133

Query: 132 EIAPEKIRGSMISMYQLMITIGILGAYLSDTAFSYTGAWRWMLGVIIIPAILLLIGVFFL 191
           E+APE IRG+MIS YQLMITIGIL A+LSDTA SY GAWRWMLGVI IP  L L+GV  L
Sbjct: 134 EVAPEHIRGAMISTYQLMITIGILVAFLSDTALSYHGAWRWMLGVIAIPGALFLLGVLGL 193

Query: 192 PDSPRWFAAKRRFVDAERVLLRLRDTSAEAKRELDEIRESLQVKQSGWALFKENSNFRRA 251
           PDSPRW   + R  +A  VL RLR       RE  +I E L+  Q GW LF EN NFRR+
Sbjct: 194 PDSPRWLMMRGRRDEAIDVLRRLRGDEVVVAREAADIEEQLKTPQRGWDLFAENPNFRRS 253

Query: 252 VFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYTNTTEQMWGTVIVGLTNVLATFIAIGLV 311
           VFLG LLQ+MQQFTGMNV+MYYAP+IF+  GY +T  QMW T +VGLTNVLATFIAI L+
Sbjct: 254 VFLGALLQIMQQFTGMNVVMYYAPRIFQEMGY-DTAAQMWFTALVGLTNVLATFIAIALI 312

Query: 312 DRWGRKPTLTLGFLVMAAGMGVLGTMMHIGIHSPSAQYFAIAMLLMFIVGFAMSAGPLIW 371
           DRWGRKP L  GF VMA G+GV+G +M+ GI+  + QY  +AMLL FIVGFAMSAGPL+W
Sbjct: 313 DRWGRKPILYTGFAVMAVGLGVVGALMNGGINGQTEQYTCVAMLLFFIVGFAMSAGPLVW 372

Query: 372 VLCSEIQPLKGRDFGITCSTATNWIANMIVGATFLTMLNTLGNANTFWVYAALNVLFILL 431
            LCSEIQPLKGRDFGI  ST TNWI NM+VG TFL++LNT+GNA+TFW+YAALN +FI+L
Sbjct: 373 TLCSEIQPLKGRDFGIGVSTFTNWITNMVVGFTFLSLLNTIGNASTFWLYAALNAVFIVL 432

Query: 432 TLWLVPETKHVSLEHIERNLMKGRKLREIG 461
           T WLVPETK V+LE IERNLM G++LR+IG
Sbjct: 433 TFWLVPETKGVTLEQIERNLMAGKRLRDIG 462


Lambda     K      H
   0.327    0.140    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: 867
Number of extensions: 37
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: 464
Length of database: 463
Length adjustment: 33
Effective length of query: 431
Effective length of database: 430
Effective search space:   185330
Effective search space used:   185330
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