GapMind for catabolism of small carbon sources

 

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

Align TctA, component of The tricarboxylate transporter, TctABC (characterized)
to candidate Pf1N1B4_3377 Tricarboxylate transport membrane protein TctA

Query= TCDB::Q9FA44
         (504 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3377
          Length = 509

 Score =  364 bits (935), Expect = e-105
 Identities = 192/505 (38%), Positives = 309/505 (61%), Gaps = 19/505 (3%)

Query: 7   LSQGFAVAMTPENLVIALIGCFVGTIVGLLPGLGPINGVAILLPLAFALHLPAESALILL 66
           L QG  + +TP ++ + +IG  +G +VG+LPGLG  NGVA+LLPL F +     SA+ILL
Sbjct: 7   LLQGMNLILTPGHIGLMVIGVLLGILVGVLPGLGAPNGVALLLPLTFTMS--PVSAIILL 64

Query: 67  ATVYIGCEYGGRISSILLNVPGDAAAIMTALDGYPMAQQGKGGVALSISAVSSFFGSLIA 126
           + +Y G  +GG I+SIL N+PG+ +++ T  DGYPMA++G+   AL+ +  S+  G+L  
Sbjct: 65  SCMYWGALFGGSITSILFNIPGEPSSVATTFDGYPMAREGRAAEALTAAFSSALIGALAG 124

Query: 127 IGGIILFAPLLAQWSLAFGPAEYFALMVFAIACLGSMMAQNPLKSFLAALIGLGLATVGV 186
           +  +   +  +A ++++F   E+FA+ + A      M    PLK+ +A +IG  +A VG+
Sbjct: 125 VLLLTFLSTKIAAFAMSFSSPEFFAVYLLAFCTFIGMSKNPPLKTVVAMMIGFAMAAVGM 184

Query: 187 DANTGVYRFTFDSVHLSDGVQFIVVVIGLFSVSEILLMLE--------HTSSGQTMVRKT 238
           D  +G  R TFD   L  G+ F V VIGLF + EIL  +E        H      ++ +T
Sbjct: 185 DTVSGNLRLTFDQPILMTGISFEVAVIGLFGIGEILCTVEEGLVFRGEHARITPMIILRT 244

Query: 239 GRMLFNLKEGAQCIGTTLRSSVIGFFVGVLPGAGATIASAITYMTEKKLSGNSDSFGKGD 298
              L       +   T +RS+++G ++G+ PG G T AS ++Y   ++ S N ++FGKG+
Sbjct: 245 WAKL------PRYWWTIVRSTLVGCWMGITPG-GPTAASFMSYSLARRFSKNRENFGKGE 297

Query: 299 IRGVAAPEAANNASACGSFIPMLTLGVPGSGTTAVMMGALTLYNITPGPAMFTEQPDIVW 358
           + GV APE A++A+   + +PMLTLG+PGS T AVM+G L ++ + PGP +F EQ D VW
Sbjct: 298 LEGVIAPETADHAAGTSALLPMLTLGIPGSATAAVMLGGLMIWGLHPGPTLFVEQHDFVW 357

Query: 359 GLIAALLIANVMLLIMNIPLIGLFTRMLTIPLWFVVPAIAAVSAVGVYAVHSTTFDLVLM 418
           GLIA++ + NV+ LI+ +  + LF  +L IP   + P I  V A+G Y+VH++ FD+VLM
Sbjct: 358 GLIASMYLGNVVSLIVVLATVPLFASILRIPFSIIAPIIIMVCAIGAYSVHNSFFDVVLM 417

Query: 419 VALGVLGYILRKMHFPMSPLILGFVLGEMLEQNLRRALSISNGNMAILWQSGVAKALLIM 478
           +  G LGY+ +K+ +P++PL+L  VLG+  E   R+++  S+G++ I W + +   L   
Sbjct: 418 LGFGALGYLFKKLGYPIAPLVLAAVLGDKAEDAFRQSMLFSDGHIGIFWSNPLVGGLTTT 477

Query: 479 AIMVIVVPPVLRLLRK--HSRKPQV 501
           A++++  P + ++L+     RKP V
Sbjct: 478 ALLMLFWPLISKVLQTLLGLRKPHV 502


Lambda     K      H
   0.326    0.141    0.414 

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: 758
Number of extensions: 39
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: 504
Length of database: 509
Length adjustment: 34
Effective length of query: 470
Effective length of database: 475
Effective search space:   223250
Effective search space used:   223250
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 (21.6 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