GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaK in Pseudomonas fluorescens FW300-N1B4

Align 4-hydroxybenzoate transporter PcaK; 4-HB transporter (characterized)
to candidate Pf1N1B4_2832 benzoate MFS transporter BenK

Query= SwissProt::Q43975
         (457 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2832
          Length = 447

 Score =  275 bits (704), Expect = 2e-78
 Identities = 154/439 (35%), Positives = 245/439 (55%), Gaps = 8/439 (1%)

Query: 19  LDAQALINDAPLSRYQWLIAIVCFLIVFVDGIDTAAMGFIAPALAQDWGVDRSQLGPVMS 78
           +D   +I++A  +R+ W++   C LI+  DG D    G + P L ++WG+   Q G + S
Sbjct: 4   IDVHEVIDNARFNRFHWMVLFWCALIIIFDGYDLVIYGVVLPMLMKEWGLSPLQAGALGS 63

Query: 79  AALGGMIIGALVSGPTADRFGRKIVLSMSMLVFGGFTLACAYSTNLDSLVIFRFLTGIGL 138
            AL GM+ GAL  GP +D+ GRK  +++ +++F GFT+   ++ N     + RF+ G+G+
Sbjct: 64  YALFGMMFGALFFGPLSDKIGRKKAITLCVMLFSGFTVLNGFARNPTEFGLCRFIAGLGI 123

Query: 139 GAAMPNATTLFSEYCPARIRSLLVTCMFCGYNLGMAIGGFISSWLIPAFGWHSLFLLGGW 198
           G  MPN   L +EY P +IRS LV  MF GY++G  +   +   LIP+FGW S+F +   
Sbjct: 124 GGVMPNVVALMNEYAPKKIRSTLVAIMFSGYSVGGMLSAGLGIVLIPSFGWQSVFYV-AV 182

Query: 199 APLILMLLVIFFLPESYRFLIVKGKNTKKVRQILSRIAPQKVQ-GVTEFHVPEEKVEAGT 257
            PL+L+ L+++FLPES  F++ +G+N ++ R +L R+ P  V     + H+ E K   GT
Sbjct: 183 LPLLLLPLIMYFLPESVGFMLRQGRN-QEARNVLERVDPAYVALASDQLHMSEVK---GT 238

Query: 258 KKGVFGMLFSAKYVKGTVLLWVTYFMGLVMIYLLTSWLPTLMRETGASLERAAFLGGLFQ 317
              V   LF       T++LW+ +F  L+M+Y L+SWLP LM   G SL  +     +  
Sbjct: 239 GTPVL-QLFREGRALRTLMLWLAFFCCLLMVYALSSWLPKLMANAGYSLGSSLSFLLVLN 297

Query: 318 FGGVLSALFIGWAMDRFNPNRIIAGFYLAAGIFAVIVGQSLSNPTLLALFILCAGIAVNG 377
           FG +  A+  G   D+ N  R++A F++ A +   ++G +   P +L L I  AG    G
Sbjct: 298 FGAIFGAVGGGVLGDKLNLPRVLAVFFVVAAVSITLLGFNSPMP-VLYLLIALAGATTIG 356

Query: 378 AQSSMPVLSARFYPTQCRATGVAWMSGIGRFGAVFGAWIGAVLLGNNWSFTMILSMLIIP 437
           +Q  +   +A+FY    R+TG+ W SGIGR GA+ G  +G  LLG +    +      +P
Sbjct: 357 SQILLYACAAQFYSMTIRSTGLGWASGIGRNGAIVGPLLGGALLGISLPLQLNFMAFALP 416

Query: 438 AAAAAIAIFVKSLVAHTDA 456
            A AA+A+ V ++ +   A
Sbjct: 417 GAVAALAMTVFAISSQRSA 435


Lambda     K      H
   0.328    0.141    0.438 

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: 628
Number of extensions: 38
Number of successful extensions: 7
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: 447
Length adjustment: 33
Effective length of query: 424
Effective length of database: 414
Effective search space:   175536
Effective search space used:   175536
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 (21.8 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