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_1905 Sulfate permease

Query= SwissProt::P0AFR2
         (559 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1905
          Length = 522

 Score =  213 bits (543), Expect = 1e-59
 Identities = 158/504 (31%), Positives = 257/504 (50%), Gaps = 39/504 (7%)

Query: 20  WKEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSR 79
           W  + T A   RDLI G++  I+A+P ++A A+ +G+ P+YGLY A +  ++  L G S 
Sbjct: 15  WLPRQTRASVGRDLIVGLSGAILALPQSIAYALIAGLPPEYGLYAAIIPVLIACLWGSSW 74

Query: 80  FSVSGPTAAFVVILY--------PVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYI 131
             + GPTAA  ++LY        P SQ + +  +L+ TLL+GIF  L+GL RFG L+ ++
Sbjct: 75  HLICGPTAAISIVLYASVSPLAVPASQDY-VTLILLLTLLAGIFQWLLGLLRFGALVNFV 133

Query: 132 PVSVTLGFTSGIGITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGIV 191
             SV LGFT G  + I   Q+ + LGL + +     L  +  LF  L  ++     +G+ 
Sbjct: 134 SHSVVLGFTLGAAVVIAIGQLPNLLGLDVPNQATA-LNSLLLLFSHLSEVDKPSLVLGLA 192

Query: 192 TLGILVFWPRLGIRLPGHLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLADGSQGNGIP 251
           T+G+ +    L  R P  L AL     ++ +   + GHV  + +              + 
Sbjct: 193 TVGVGIALKLLVPRWPTLLIALALSGLLVWLWPAMFGHVQLVSAF-------------VG 239

Query: 252 QLLPQLVLPWDLPNSEFTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTKHKAN 311
           +L P   LP DL         D +  LLP+A ++ MLG + SL  A  L   +     AN
Sbjct: 240 RLPPFSPLPLDL---------DLVLRLLPSAVAVGMLGLVTSLSIARSLSARSQQLLDAN 290

Query: 312 SELVGQGLGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALLVLAPLL 371
            E+  QG  N++  FF G  +  +  RSA +  AGA SP++ V  ++ V L  +  A L+
Sbjct: 291 QEVRAQGFSNMVGAFFSGSLSAGSFTRSALSYDAGACSPLAGVFSAMWVALFAIFGAVLI 350

Query: 372 SWLPLSAMAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIAISVGI 431
           + +P+ AMA  +L++AW + +   +  LLR +  + +++ L C++ T+L ++  AI  G 
Sbjct: 351 AHIPIPAMAGSILLIAWGLVDHRGIRALLRVSRAEFLVMALTCVA-TLLLELQTAIYAG- 408

Query: 432 VLASLLFMRRIARMTRLAPVVVDVPDDVLVLRVIGPLFFAAAEGLFTDLESRLEGKRIVI 491
           VLASL F  +     R+        D   +LRV G +FF A+  L   L+ R+ G R+VI
Sbjct: 409 VLASLFFYLKRTSQPRVQHWREGDED---ILRVGGSIFFGASHYLQVRLQ-RMHGARVVI 464

Query: 492 LKWDAVPVLDAGGLDAFQRFVKRL 515
            +   +  +D  G++   +  +RL
Sbjct: 465 -EAQQINFIDYSGVEMLHQEARRL 487


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: 639
Number of extensions: 37
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: 522
Length adjustment: 35
Effective length of query: 524
Effective length of database: 487
Effective search space:   255188
Effective search space used:   255188
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: 52 (24.6 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