GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tctA in Pseudomonas stutzeri RCH2

Align TctA, component of The tricarboxylate transporter, TctABC (characterized)
to candidate GFF369 Psest_0370 Uncharacterized protein conserved in bacteria

Query= TCDB::Q9FA44
         (504 letters)



>FitnessBrowser__psRCH2:GFF369
          Length = 506

 Score =  342 bits (876), Expect = 2e-98
 Identities = 180/484 (37%), Positives = 288/484 (59%), Gaps = 8/484 (1%)

Query: 7   LSQGFAVAMTPENLVIALIGCFVGTIVGLLPGLGPINGVAILLPLAFALHLPAESALILL 66
           L QGF    +   L++ L G  VG + G +PGL     VA+ LPL F +    ++ L LL
Sbjct: 5   LQQGFGAVFSLNILLLMLGGVAVGIVFGAVPGLSATMAVALCLPLTFTMG--PQAGLSLL 62

Query: 67  ATVYIGCEYGGRISSILLNVPGDAAAIMTALDGYPMAQQGKGGVALSISAVSSFFGSLIA 126
             ++IG   GG IS+ILL +PG  ++I T  DG P+ +QG G  AL +  V SF G++ +
Sbjct: 63  VALFIGATSGGLISAILLKIPGTPSSIATVFDGGPLMEQGMGVKALGVGIVFSFLGTIFS 122

Query: 127 IGGIILFAPLLAQWSLAFGPAEYFALMVFAIACLGSMMAQNPLKSFLAALIGLGLATVGV 186
           I  ++  AP LA+ +L+FGP EYFA+ VF++  + ++ A + +K   A  +G+ ++TVG+
Sbjct: 123 IIALMFIAPQLAKVALSFGPHEYFAIAVFSLTLIATLSAGSMVKGLFAGTLGIAVSTVGI 182

Query: 187 DANTGVYRFTFDSVHLSDGVQFIVVVIGLFSVSEILLMLE------HTSSGQTMVRKTGR 240
                V RFTF    L+ G   + V+IG+F+V+E++ + E         +G   +++   
Sbjct: 183 APVEAVRRFTFGVSELNGGFSMLTVMIGMFAVAEVIKLAETGRHAVRNKAGSVSMKQIKG 242

Query: 241 MLFNLKEGAQCIGTTLRSSVIGFFVGVLPGAGATIASAITYMTEKKLSGNSDSFGKGDIR 300
             F+LKE  Q +    RS +IG  VG+LPG GA  ++ ++Y+  KK +   +++GKG+I 
Sbjct: 243 FGFSLKEFRQELPNATRSGLIGLAVGILPGIGAGTSNLLSYIVAKKRAKQPETYGKGNIG 302

Query: 301 GVAAPEAANNASACGSFIPMLTLGVPGSGTTAVMMGALTLYNITPGPAMFTEQPDIVWGL 360
           GV A E ANNA   G+ +P++TLG+PG  TTA+++G   ++ I PGP +F  Q  +V+ +
Sbjct: 303 GVVASETANNAGIGGAMMPLMTLGIPGDTTTAILLGGFLIHGIQPGPLLFISQGPLVYTI 362

Query: 361 IAALLIANVMLLIMNIPLIGLFTRMLTIPLWFVVPAIAAVSAVGVYAVHSTTFDLVLMVA 420
            AALL+A+VM+L M    + LF ++L +P   ++P I  +  VG + + S  FD+  ++ 
Sbjct: 363 FAALLVASVMMLFMEFYGLRLFIKLLDVPKHILLPIILVLCVVGAFGLSSRLFDVWSILL 422

Query: 421 LGVLGYILRKMHFPMSPLILGFVLGEMLEQNLRRALSISNGNMAILWQSGVAKALLIMAI 480
            GVLGY   K   P++P I+GF+LG M E NLRR L +S+GN A  + + +A   L +A+
Sbjct: 423 FGVLGYGFVKAGMPVAPFIIGFILGPMAETNLRRGLMLSDGNFASFFTNPIAATFLGLAL 482

Query: 481 MVIV 484
             ++
Sbjct: 483 AFVL 486


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: 856
Number of extensions: 47
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: 506
Length adjustment: 34
Effective length of query: 470
Effective length of database: 472
Effective search space:   221840
Effective search space used:   221840
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