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

GapMind for catabolism of small carbon sources

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

Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate AO356_16580 AO356_16580 transporter

Query= SwissProt::P0AFR2
         (559 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_16580
          Length = 579

 Score =  532 bits (1371), Expect = e-155
 Identities = 279/505 (55%), Positives = 373/505 (73%), Gaps = 13/505 (2%)

Query: 20  WKEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSR 79
           W+  YT  R   DL+AG+TVGIIAIPLAMALAI  GV PQ+GLYT  VA  +IALTGGSR
Sbjct: 16  WRAGYTLERLRGDLVAGLTVGIIAIPLAMALAIAVGVPPQHGLYTVLVAAPLIALTGGSR 75

Query: 80  FSVSGPTAAFVVILYPVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYIPVSVTLGF 139
           F+VSGPTAAFVVIL P++QQ+GL GLL+ T+L+G+ LI +GL R GRLI+YIP  V LGF
Sbjct: 76  FNVSGPTAAFVVILLPITQQYGLGGLLLCTMLAGLILIALGLIRAGRLIQYIPYPVILGF 135

Query: 140 TSGIGITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGIVTLGILVFW 199
           T+GIG+ I T+Q+KD LGL  A   +HY++++G L +ALP   +GD  IG V L +L+ W
Sbjct: 136 TAGIGVVIATLQLKDLLGLTTAGQAKHYIEQLGELIVALPGARLGDGVIGAVCLAVLIVW 195

Query: 200 PRLGIRLPGHLPALLAGCAVMGIVNLLGG-HVATIGSQFHYVLADGSQGNGIPQLLPQLV 258
           PR   R+PGHL ALL G  ++G+    GG  +AT+G +F YV+ DG    GIP  LP   
Sbjct: 196 PRWVPRVPGHLVALLVG-TLLGLAMERGGWPIATLGERFSYVV-DGIAHPGIPPFLPSFD 253

Query: 259 LPWDLPNSE---FTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTKHKANSELV 315
            PW+LP+S+     L++D IR LL  AF++AMLGAIESLLCAVV DGMTG+KH  N+EL+
Sbjct: 254 WPWNLPDSQGHPLILSYDLIRQLLAPAFAIAMLGAIESLLCAVVADGMTGSKHDPNAELM 313

Query: 316 GQGLGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALLVLAPLLSWLP 375
           GQGLGN++AP FGGITATAAIARSA NVR+GA SP++A+IHS++V++A+++LAPL S+LP
Sbjct: 314 GQGLGNLVAPLFGGITATAAIARSATNVRSGAFSPLAAIIHSLVVLVAIVLLAPLFSYLP 373

Query: 376 LSAMAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIAISVGIVLAS 435
           ++A+AALL+MVAWNMSEA  V+  LR AP+ D++V+L C+ LTVLFDMV+A++VG++LA+
Sbjct: 374 MAALAALLVMVAWNMSEAGHVLHTLRIAPRSDVLVLLTCLGLTVLFDMVLAVAVGLLLAA 433

Query: 436 LLFMRRIARMTRLAPV-------VVDVPDDVLVLRVIGPLFFAAAEGLFTDLESRLEGKR 488
            LF++R++ +T  A +       ++D+P+ V    + GPLFF AAE     L     G R
Sbjct: 434 GLFIKRMSELTDSAELPRHFHQALLDMPEHVRCYAIRGPLFFGAAEKALDVLRRFDPGVR 493

Query: 489 IVILKWDAVPVLDAGGLDAFQRFVK 513
           +V+++  AVP+LD   L A +  +K
Sbjct: 494 VVVVEMSAVPMLDMTALAALENILK 518


Lambda     K      H
   0.328    0.142    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: 823
Number of extensions: 44
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: 559
Length of database: 579
Length adjustment: 36
Effective length of query: 523
Effective length of database: 543
Effective search space:   283989
Effective search space used:   283989
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: 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