GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Klebsiella michiganensis M5al

Align C4-dicarboxylate transporter (substrates: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate, mesaconate) (characterized)
to candidate BWI76_RS08460 BWI76_RS08460 dicarboxylate/amino acid:cation symporter

Query= TCDB::Q01857
         (444 letters)



>FitnessBrowser__Koxy:BWI76_RS08460
          Length = 435

 Score =  275 bits (703), Expect = 2e-78
 Identities = 147/364 (40%), Positives = 226/364 (62%), Gaps = 5/364 (1%)

Query: 54  FIKLVKMIIAPVIFLTVATGIAGMSDLQKVGRVAGKAMLYFLTFSTLALIIGLIVANVVQ 113
           F+++VKMIIAP++  T+  GIA M D + +GR+  K    F+  S L++ +GL++ N+ Q
Sbjct: 47  FLRMVKMIIAPLVISTLVVGIAKMGDAKTLGRIFSKTFFLFICASLLSIALGLVIVNLFQ 106

Query: 114 PGAGMNIDPASLDPAAVATFAAKAHEQSIVGFLTNIIPTTIVGAFADGDILQVLFFSVLF 173
           PGAG+N  P   D  AVA  A ++   ++  F+++ +PT+IV A A  +ILQ++ FS+  
Sbjct: 107 PGAGINFVPH--DAGAVA--AVQSEPFTLKVFISHAVPTSIVDAMARNEILQIVVFSIFL 162

Query: 174 GIALAMVGEKGEQVVNFLNSLTAPVFKLVAILMKAAPIGAFGAMAFTIGKYGVGSIANLA 233
           G +LA +GEK E +V  L+SL   + KL   +M  AP+  F A++  I + G+G + +  
Sbjct: 163 GCSLAAIGEKAEPIVKVLDSLVHVMLKLTGYVMLFAPLTVFAAISGLIAERGLGVMVSAG 222

Query: 234 MLIGTFYITSLLFVFIVLGAVARYNGFSIVALLRYIKEELLLVLGTSSSEAALPGLMNKM 293
           + +G FY+T  +   I++G      G  I  L + I E  LL   TSSSEAA PG ++K+
Sbjct: 223 IFMGEFYLTLGMLWAILIGLSTVIVGPCISRLTKAIFEPALLAFTTSSSEAAFPGTLDKL 282

Query: 294 EKAGCKRSVVGLVIPTGYSFNLDGTNIYMTLAALFIAQATGIHLSWGDQILLLLVAMLSS 353
           EK G    +   V+P GYSFNL G+  Y + A +FIAQA  +HLS G+QI +LL+ ML+S
Sbjct: 283 EKFGVSSKIASFVLPIGYSFNLVGSMAYCSFATVFIAQACNVHLSMGEQITMLLILMLTS 342

Query: 354 KGAAGITGAGFITLAATLSVVPSVPVAGMALILGIDRFMSECRALTNLVGNAVATIVVAR 413
           KG AG+  A  + +AATL+   ++P AG+ L++G+D F+   R+ TN++ NA+   +V R
Sbjct: 343 KGMAGVPRASMVVIAATLNQF-NIPEAGLILLMGVDPFLDMGRSATNVMSNAMGAAIVGR 401

Query: 414 WENE 417
           WE E
Sbjct: 402 WEGE 405



 Score = 25.4 bits (54), Expect = 0.004
 Identities = 48/210 (22%), Positives = 83/210 (39%), Gaps = 51/210 (24%)

Query: 28  VAIAAGILLGHFYPELGTQLKPLGDAFIKLVKMIIAPVIFLTVATGIAGMSDLQKVGRVA 87
           V ++AGI +G FY  LG     L    I L  +I+ P I           S L K   + 
Sbjct: 217 VMVSAGIFMGEFYLTLGM----LWAILIGLSTVIVGPCI-----------SRLTKA--IF 259

Query: 88  GKAMLYFLTFSTLALIIGLIVANVVQPGAGMNIDPASLDPAAVATFAAKAHEQSIVGFLT 147
             A+L F T S+ A            PG    ++   +  + +A+F         +G+  
Sbjct: 260 EPALLAFTTSSSEAAF----------PGTLDKLEKFGVS-SKIASFVLP------IGYSF 302

Query: 148 NIIPTTIVGAFADGDILQVLFFSVLFGIALAMVGEKGEQVVNFLNSLTAPVFKLVAILMK 207
           N++ +    +FA       +F +    + L+M    GEQ+   L      +  L +  M 
Sbjct: 303 NLVGSMAYCSFA------TVFIAQACNVHLSM----GEQITMLL------ILMLTSKGMA 346

Query: 208 AAPIGAFGAMAFTIGKYGVGSIANLAMLIG 237
             P  +   +A T+ ++ +   A L +L+G
Sbjct: 347 GVPRASMVVIAATLNQFNIPE-AGLILLMG 375


Lambda     K      H
   0.324    0.139    0.393 

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: 510
Number of extensions: 27
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 444
Length of database: 435
Length adjustment: 32
Effective length of query: 412
Effective length of database: 403
Effective search space:   166036
Effective search space used:   166036
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.3 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