GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylT in Pseudomonas fluorescens FW300-N2C3

Align D-xylose transporter; D-xylose-proton symporter (characterized)
to candidate AO356_27270 AO356_27270 MFS transporter

Query= SwissProt::O52733
         (457 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_27270
          Length = 472

 Score =  302 bits (774), Expect = 1e-86
 Identities = 161/443 (36%), Positives = 258/443 (58%), Gaps = 12/443 (2%)

Query: 9   VYFFGALGGLLFGYDTGVISGAILFIQKQMNLGSWQQGWVVSAVLLGAILGAAIIGPSSD 68
           + +    GGLLFG+DTGVI+GA+L+++  + L  + +G V SA+L+GA++GA   G  SD
Sbjct: 31  ITWIATFGGLLFGFDTGVINGALLYMKDDLGLTPFTEGLVASALLIGAMMGALFSGRLSD 90

Query: 69  RFGRRKLLLLSAIIFFVGALGSAFSPEFWTLIISRIILGMAVGAASALIPTYLAELAPSD 128
             GRR+++L  A++FF+GAL  A +P    ++ +R  LG+AVG AS ++P YLAE+APS 
Sbjct: 91  LKGRRRIILFLAVVFFLGALACALAPTLNVMVAARFTLGLAVGGASVVVPAYLAEMAPSS 150

Query: 129 KRGTVSSLFQLMVMTGILLAYITNYSFSGFYTG----WRWMLGFAAIPAALLFLGGLILP 184
            RG + +  +LM++TG  LA+ TN +    ++     WRWML  A +PA  L+LG L +P
Sbjct: 151 IRGRIITRNELMIVTGQFLAFTTNATLGNLFSDLDGVWRWMLALATLPAVALWLGMLYMP 210

Query: 185 ESPRFLVKSGHLDEARHVLDTMNKHDQVAVNKE--INDIQESAKIVSGGWSELFGKMVRP 242
           ESPR+L   G   E   VL  + +        E     I     I  GGW +L  K  R 
Sbjct: 211 ESPRWLATKGRFREGLEVLKLVREEYYAKAEMEAITQQISNERFIKKGGWRDLSQKGARR 270

Query: 243 SLIIGIGLAIFQQVMGCNTVLYYAPTIFTDVGFGVSAALLAHIGIGIFNVIVTAIAVAIM 302
             +IGIG+A+  Q+ G N+++Y+   I T+ G    +AL+A++  G+ ++  T + +A++
Sbjct: 271 IFLIGIGIAVTSQLTGVNSIMYFGTQILTEAGLEQRSALIANVVNGVISIGATFVGIALL 330

Query: 303 DKIDRKKIVNIGAVGMGISLFVMSIGMKFSGGSQTAAIISVIALTVYIAFFSATWGPVMW 362
           D++ R+ ++ +G  G  +SL ++ +   F   S T A++ + A+ +++A      GP  W
Sbjct: 331 DRVGRRPMMLLGFTGTTLSLLLIGLVSVFVDPSVTRAMLILGAMAMFLASMQGLIGPAFW 390

Query: 363 VMIGEVFPLNIRGLGNSFASVINWTANMIVSLTFPSLLDFFGTGS---LFIGYGILCFAS 419
           V++ E+FP+ IRG     A    W  N+++ + FPSL+   G G    +F+G G+L   S
Sbjct: 391 VLLAEIFPMRIRGGCMGMAIAAFWLTNVMIGMFFPSLVATIGIGQTFFVFVGAGLL---S 447

Query: 420 IWFVQKKVFETRNRSLEDIEATL 442
           + FV   V ETR  +LE+IE  L
Sbjct: 448 LTFVAVWVPETRGSTLEEIEQRL 470


Lambda     K      H
   0.327    0.141    0.424 

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: 577
Number of extensions: 33
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: 457
Length of database: 472
Length adjustment: 33
Effective length of query: 424
Effective length of database: 439
Effective search space:   186136
Effective search space used:   186136
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