GapMind for catabolism of small carbon sources

 

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

Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate Pf1N1B4_2936 Putative sulfate permease

Query= SwissProt::P0AFR2
         (559 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2936
          Length = 573

 Score =  531 bits (1368), Expect = e-155
 Identities = 289/548 (52%), Positives = 382/548 (69%), Gaps = 14/548 (2%)

Query: 20  WKEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSR 79
           W+  Y+  R   D+ AG+TVGIIAIPLAMALAI  GVAPQ GLYT  +A  +IALTGGSR
Sbjct: 16  WRAGYSLRRLRGDISAGVTVGIIAIPLAMALAIAVGVAPQQGLYTVLIAAPLIALTGGSR 75

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

Query: 140 TSGIGITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGIVTLGILVFW 199
           T+GIGI I T+Q+KD LGL      EHY++++G L  ALP+  +GD  IG++ L +L+ W
Sbjct: 136 TAGIGIVIATLQLKDLLGLSTTGHAEHYIEQLGGLLQALPSARLGDGIIGVMCLAVLIVW 195

Query: 200 PRLGIRLPGHLPALLAGCAVMGIVNLLGG-HVATIGSQFHYVLADGSQGNGIPQLLPQLV 258
           PR   R+PGHL AL  G A++G+    GG  VAT+G +F Y++ DG    GIP  LP   
Sbjct: 196 PRFVPRIPGHLVALAVG-ALLGVALESGGLAVATLGERFSYIV-DGVSHPGIPPFLPSFD 253

Query: 259 LPWDLP---NSEFTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTKHKANSELV 315
            PW+LP        L++D IR L+  AF++AMLGAIESLLCAVV DGMTG+KH  N+EL+
Sbjct: 254 WPWNLPGPYGQPLHLSYDLIRQLMAPAFAIAMLGAIESLLCAVVADGMTGSKHDPNAELL 313

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

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

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

Query: 489 IVILKWDAVPVLDAGGLDAFQRFVKRL-PEGCELRVCNVEFQPLRTMARAGIQPIPGRLA 547
           +VI++  AVP+LD   L AF   ++    +G  L +     +    + RAGI     +LA
Sbjct: 494 VVIVEMSAVPMLDMTALAAFDNILRDYRTDGIGLILVGTAPRVRLKLRRAGIHREQRQLA 553

Query: 548 FFPNRRAA 555
           +  N   A
Sbjct: 554 YVNNLEQA 561


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: 812
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: 559
Length of database: 573
Length adjustment: 36
Effective length of query: 523
Effective length of database: 537
Effective search space:   280851
Effective search space used:   280851
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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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