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

GapMind for catabolism of small carbon sources

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

Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate Pf1N1B4_5961 Major facilitator superfamily transporter

Query= TCDB::F8SVK1
         (552 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5961
          Length = 558

 Score =  785 bits (2028), Expect = 0.0
 Identities = 382/550 (69%), Positives = 460/550 (83%), Gaps = 3/550 (0%)

Query: 3   TVSGQISHAPMTKEEKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFIFT 62
           T +G   H  +T+EE++VIFASSLGTVFEWYDFYL GSLAA I+K FF+GVN T +FIF 
Sbjct: 7   TTTGSAPHHGITREERKVIFASSLGTVFEWYDFYLYGSLAAIIAKHFFAGVNETTSFIFA 66

Query: 63  LLGFAAGFAVRPFGALVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMASPV 122
           LL FAAGFAVRPFGA+VFGRLGDM+GRK+TFLITIVIMG+ST VVGFLPGYA IG+A+P+
Sbjct: 67  LLAFAAGFAVRPFGAIVFGRLGDMIGRKHTFLITIVIMGISTAVVGFLPGYATIGVAAPI 126

Query: 123 IFIAMRLLQGLALGGEYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGVRT 182
           I I +RLLQGLALGGEYGGAATYVAEHAP  +RG++T+WIQTTATLGLFLSLLVIL  RT
Sbjct: 127 ILITLRLLQGLALGGEYGGAATYVAEHAPKGKRGYFTSWIQTTATLGLFLSLLVILACRT 186

Query: 183 AMGEDAFGAWGWRIPFVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLSEAFGQW 242
            +G +AF AWGWRIPF+ S++LL +SV+IR+QL ESP F ++K EGK+SKAPL+E+F +W
Sbjct: 187 ILGNEAFEAWGWRIPFLLSILLLIVSVYIRLQLSESPVFLKMKEEGKSSKAPLTESFARW 246

Query: 243 KNLKIVILALIGVTAGQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIGTPFFLF 302
           +NLKIVI+AL+G TAGQAVVWYTGQFYALFFL QTLK+D  +AN LIA +LLIGTPFF+ 
Sbjct: 247 ENLKIVIMALLGGTAGQAVVWYTGQFYALFFLLQTLKIDPQTANFLIAGSLLIGTPFFII 306

Query: 303 FGSLSDRIGRKPIILAGCLIAALTYFPLFKALTHYANPALEAATQKSPIVVIANPDECSF 362
           FGSLSDRIGRK II+AGC+IAALTYFP+F ALT Y NP + AA +K+P+ VIA P +CSF
Sbjct: 307 FGSLSDRIGRKGIIMAGCVIAALTYFPIFHALTEYGNPDVFAAQEKNPVTVIAAPGQCSF 366

Query: 363 QFNPVGTSKFTSSCDIAKSALSKAGLNYDNVAAPAGTLAQIKVGDTTIDTYDG---KAAD 419
           QF+PVG +KFTSSCD+AK+ L+K  + Y+NV A  G +AQ+++GD  I +++G    AAD
Sbjct: 367 QFDPVGKAKFTSSCDLAKTVLAKKAIPYENVKAEPGAIAQVRIGDKVIQSFEGTGMPAAD 426

Query: 420 AKDAGKAFDKNLGTALKAASYPPKADPSQLNWPMTVVILTILVIYVTMVYGPIAAMLVEM 479
            K    AF   LGTALK A YP KADP++ N+PM +++LTILVIYVTMVYGPIAA LVE+
Sbjct: 427 FKARNDAFVATLGTALKDAGYPEKADPAKTNYPMVLLLLTILVIYVTMVYGPIAAWLVEL 486

Query: 480 FPTRIRYTSMSLPYHIGNGWFGGFLPATAFAIVAAKGNIYSGLWYPIIIALATFVIGLLF 539
           FP RIRYTSMSLPYHIGNGWFGGFLP  AFA+VAA G+IY GLWYPI+IA+ T ++G  F
Sbjct: 487 FPARIRYTSMSLPYHIGNGWFGGFLPTVAFAMVAATGDIYYGLWYPIVIAVMTAILGTFF 546

Query: 540 VRETKDSNIY 549
           + ETKD  I+
Sbjct: 547 LPETKDREIH 556


Lambda     K      H
   0.325    0.139    0.422 

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: 918
Number of extensions: 40
Number of successful extensions: 5
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: 552
Length of database: 558
Length adjustment: 36
Effective length of query: 516
Effective length of database: 522
Effective search space:   269352
Effective search space used:   269352
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 (21.6 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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
the source code
instructions for running GapMind on your computer

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