Aligments for a candidate for xylT in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Aligments for a candidate for xylT in Dyella japonica UNC79MFTsu3.2

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

Query= SwissProt::P0AE24
         (472 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_1228 N515DRAFT_1228 MFS
           transporter, SP family, galactose:H+ symporter
          Length = 463

 Score =  504 bits (1299), Expect = e-147
 Identities = 265/468 (56%), Positives = 336/468 (71%), Gaps = 6/468 (1%)

Query: 4   INTESALTPRSLRDTRRMNMFVSVAAAVAGLLFGLDIGVIAGALPFITDHFVLTSRLQEW 63
           +N+++  TP +    +   ++  V AA+AGL+FGLDIGVI+GA  FI   F ++    EW
Sbjct: 1   MNSQAIATPTA--HVKGTVIYTCVLAALAGLMFGLDIGVISGASQFIKAEFAISDHTIEW 58

Query: 64  VVSSMMLGAAIGALFNGWLSFRLGRKYSLMAGAILFVLGSIGSAFATSVEMLIAARVVLG 123
           +VSSMM GAA+GAL  GWLS  LGRK SL+ GAILFV+GS+    A S E LIAARV+LG
Sbjct: 59  IVSSMMFGAAVGALGAGWLSSHLGRKRSLILGAILFVIGSLLCGLAWSPETLIAARVILG 118

Query: 124 IAVGIASYTAPLYLSEMASENVRGKMISMYQLMVTLGIVLAFLSDTAFSYSGNWRAMLGV 183
           +A+GIA++TAPLYL+E+A E++RG MIS YQLM+T+GI++AFLSDTA SY G WR MLGV
Sbjct: 119 LAIGIATFTAPLYLAEVAPEHIRGAMISTYQLMITIGILVAFLSDTALSYHGAWRWMLGV 178

Query: 184 LALPAVLLIILVVFLPNSPRWLAEKGRHIEAEEVLRMLRDTSEKAREELNEIRESLKLKQ 243
           +A+P  L ++ V+ LP+SPRWL  +GR  EA +VLR LR        E  +I E LK  Q
Sbjct: 179 IAIPGALFLLGVLGLPDSPRWLMMRGRRDEAIDVLRRLRGDEVVVAREAADIEEQLKTPQ 238

Query: 244 GGWALFKINRNVRRAVFLGMLLQAMQQFTGMNIIMYYAPRIFKMAGFTTTEQQMIATLVV 303
            GW LF  N N RR+VFLG LLQ MQQFTGMN++MYYAPRIF+  G+ T   QM  T +V
Sbjct: 239 RGWDLFAENPNFRRSVFLGALLQIMQQFTGMNVVMYYAPRIFQEMGYDTA-AQMWFTALV 297

Query: 304 GLTFMFATFIAVFTVDKAGRKPALKIGFSVMALGTLVLGYCLMQFDNGTASSGLSWLSVG 363
           GLT + ATFIA+  +D+ GRKP L  GF+VMA+G  V+G  +    NG       +  V 
Sbjct: 298 GLTNVLATFIAIALIDRWGRKPILYTGFAVMAVGLGVVGALMNGGINGQTE---QYTCVA 354

Query: 364 MTMMCIAGYAMSAAPVVWILCSEIQPLKCRDFGITCSTTTNWVSNMIIGATFLTLLDSIG 423
           M +  I G+AMSA P+VW LCSEIQPLK RDFGI  ST TNW++NM++G TFL+LL++IG
Sbjct: 355 MLLFFIVGFAMSAGPLVWTLCSEIQPLKGRDFGIGVSTFTNWITNMVVGFTFLSLLNTIG 414

Query: 424 AAGTFWLYTALNIAFVGITFWLIPETKNVTLEHIERKLMAGEKLRNIG 471
            A TFWLY ALN  F+ +TFWL+PETK VTLE IER LMAG++LR+IG
Sbjct: 415 NASTFWLYAALNAVFIVLTFWLVPETKGVTLEQIERNLMAGKRLRDIG 462


Lambda     K      H
   0.327    0.138    0.409 

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: 778
Number of extensions: 42
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: 472
Length of database: 463
Length adjustment: 33
Effective length of query: 439
Effective length of database: 430
Effective search space:   188770
Effective search space used:   188770
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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources