GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tctA in Cupriavidus basilensis 4G11

Align TctA, component of The tricarboxylate transporter, TctABC (characterized)
to candidate RR42_RS03695 RR42_RS03695 hypothetical protein

Query= TCDB::Q9FA44
         (504 letters)



>FitnessBrowser__Cup4G11:RR42_RS03695
          Length = 500

 Score =  400 bits (1028), Expect = e-116
 Identities = 199/498 (39%), Positives = 320/498 (64%), Gaps = 4/498 (0%)

Query: 1   MDTWIYLSQGFAVAMTPENLVIALIGCFVGTIVGLLPGLGPINGVAILLPLAFALHLPAE 60
           M+ + +L+ GF+ A+T +N+    +GC +GT++G+LPG+GP+  +A+LLP+ + L  P  
Sbjct: 1   MELFEHLALGFSTALTLQNVGYCFLGCVLGTLIGVLPGIGPLATIAMLLPVTYTL--PPV 58

Query: 61  SALILLATVYIGCEYGGRISSILLNVPGDAAAIMTALDGYPMAQQGKGGVALSISAVSSF 120
           +ALI+LA +Y G +YGG  ++IL+N+PG++++++T +DGY MA++G+ GVAL+ + + SF
Sbjct: 59  AALIMLAGIYYGAQYGGSTTAILVNLPGESSSVVTTIDGYQMARRGRAGVALATAGLGSF 118

Query: 121 FGSLIAIGGIILFAPLLAQWSLAFGPAEYFALMVFAIACLGSMMAQNPLKSFLAALIGLG 180
           F   +A   +  FA  L++ +  FGPAEYF+LM   +     + + +  K+    ++GL 
Sbjct: 119 FAGCVATLILAAFATPLSELAFKFGPAEYFSLMCLGLIGAVVLASGSLPKAVAMIVLGLL 178

Query: 181 LATVGVDANTGVYRFTFDSVHLSDGVQFIVVVIGLFSVSEILLMLEHTSSGQTMVRKTGR 240
           L  VG D N+G  RF+FD   L+DGV F+ + +G+F  +EI+  LE   + +T       
Sbjct: 179 LGLVGTDVNSGAARFSFDVPELTDGVDFVALAMGMFGFAEIIANLEQKENRETFTDHVSN 238

Query: 241 MLFNLKEGAQCIGTTLRSSVIGFFVGVLPGAGATIASAITYMTEKKLSGNSDSFGKGDIR 300
           +  +  +  +     LR + +G  +G+LPG GA +AS   Y  EKK S  S  FGKG I 
Sbjct: 239 LWPSRADFKRMAPAVLRGTALGSILGILPGGGAALASFAAYSLEKKTSKYSHEFGKGAIE 298

Query: 301 GVAAPEAANNASACGSFIPMLTLGVPGSGTTAVMMGALTLYNITPGPAMFTEQPDIVWGL 360
           GVA PE+ANNA+A  SFIP+LTLG+P +   A+M+GA+T++NI PGP + T  P + WGL
Sbjct: 299 GVAGPESANNAAAQTSFIPLLTLGIPPNAVMALMVGAMTIHNIQPGPQVMTSNPALFWGL 358

Query: 361 IAALLIANVMLLIMNIPLIGLFTRMLTIPLWFVVPAIAAVSAVGVYAVHSTTFDLVLMVA 420
           IA++ I N+ML+I+N+PLIG++ ++L +P  ++ PAI     +GV++V++ TFD+     
Sbjct: 359 IASMWIGNLMLIILNLPLIGIWVKLLQVPYRYLYPAILVFCCIGVFSVNNQTFDVFTAAG 418

Query: 421 LGVLGYILRKMHFPMSPLILGFVLGEMLEQNLRRALSISNGNMAILWQSGVAKALLIMA- 479
            GV+GY+  K+    +PL+LGFVLG M+E+N RRAL +S G   +     ++  LLI A 
Sbjct: 419 FGVIGYLFIKLKCEPAPLLLGFVLGPMMEENFRRALLLSRGTFTVFLTRPLSLGLLIAAG 478

Query: 480 -IMVIVVPPVLRLLRKHS 496
            ++ IV  P ++  R+ +
Sbjct: 479 LLVCIVALPSIKAKREEA 496


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: 741
Number of extensions: 37
Number of successful extensions: 5
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: 500
Length adjustment: 34
Effective length of query: 470
Effective length of database: 466
Effective search space:   219020
Effective search space used:   219020
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