GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lctP in Desulfovibrio vulgaris Hildenborough

Align L-lactate permease (characterized, see rationale)
to candidate 208540 DVU3026 L-lactate permease family protein

Query= uniprot:L0GFN1
         (564 letters)



>MicrobesOnline__882:208540
          Length = 570

 Score =  478 bits (1229), Expect = e-139
 Identities = 256/569 (44%), Positives = 355/569 (62%), Gaps = 20/569 (3%)

Query: 1   MSNGLLALFAFTPILLAAIMLIGLRWPASRAMPLVFLFTAAIGLFVWDMSVNRIIASTLQ 60
           MS  LLAL A  PIL+A ++++G+RWPA++AMPL +L      + VW++    + A TLQ
Sbjct: 1   MSLELLALVALLPILVALVLMVGMRWPATKAMPLSWLVCVLGAIGVWNLPAGYVTALTLQ 60

Query: 61  GLVITLGLLWIIFGAILLLNTLKHSGGITAIRAGFTTISPDRRIQAIIIAWLFGCFIEGA 120
           G+V  +G+L I+FGAI++L TL++SGG+  I+ G   +S D+RIQAIII ++F  FIEGA
Sbjct: 61  GIVTAIGVLIIVFGAIIILYTLQYSGGMETIQYGMQNVSRDKRIQAIIIGYMFAAFIEGA 120

Query: 121 SGFGTPAAIAAPLLVAVGFPAMAAVLLGMLVQSTPVSFGAVGTPIVVG-------INSGL 173
           +GFGTPAA+AAPLL+++GFP +AA ++ ++  S  VSFGAVGTPI++G       +   +
Sbjct: 121 AGFGTPAALAAPLLLSLGFPPLAAAVICLVFNSFCVSFGAVGTPILIGLKFLAPLVKDAV 180

Query: 174 DTATIGAQLVAQGSSWNAYLQQITSSVAITHAIVGTVMPLVMVLMLTRFFGKEKSWKAGF 233
              T G      GS    + + I     I H  +  ++P+ M+  LTRF+G+ KSW  GF
Sbjct: 181 TAGTPGLNFTDFGS----FAKVIGQWATIMHGFMIVILPIFMLGFLTRFYGQNKSWSEGF 236

Query: 234 EVLPFAIFAGLAFTLPYAATGIFLGPEFPSLLGGLVGLAIVTTAARFKFLTPKTTWDFAD 293
           +   F +FA ++F +PY     F+GPEFPSL+GGLVGL I+   A+  F  P+ TWDF  
Sbjct: 237 KAWKFCVFAAVSFAVPYFIFAWFVGPEFPSLIGGLVGLGIIVAGAKRGFCVPEETWDFGP 296

Query: 294 AKEWPAEWLGTIEMKLDEMAARPMSAFRAWLPYVLVGAILVISRVFPQ--VTAALKSVSI 351
              W  EW GTI+          MS F+AWLPY+L+GAILV++RV P   +   L +  I
Sbjct: 297 QSTWDPEWTGTIKTAAKTEFKAHMSQFKAWLPYILIGAILVVTRV-PSLGLKGFLSAQKI 355

Query: 352 AFANILGETGINAGIEPLYLPGGI-LVMVVLITFFLHGMRVSELKAAVKESSGVLLSAGF 410
            F NILG  G++A I+ LYLPG I   +V L+T  LHGM    +K A  ES   + +   
Sbjct: 356 PFDNILGFKGVSASIDYLYLPGTIPFTLVALLTILLHGMSGDAVKRAWSESFAKMKAPTI 415

Query: 411 VLLFTVPMVRILINSGV-----NGAELASMPIVMARYVADSVGSIYPLLAPAVGALGAFL 465
            L F V +V I   SGV     N     SMP+ MA+ VA   G+ +P+LA  VG LGAF+
Sbjct: 416 ALFFAVALVSIFRGSGVADVALNPNNYPSMPLAMAKAVAALAGNAWPMLASYVGGLGAFI 475

Query: 466 AGSNTVSNMMFSQFQFGVAQSLGISGAMVVATQAVGAAAGNMVAIHNVVAASATVGLLGR 525
            GSNTVS+++F++FQ+GVA  L +   ++VA Q VG A GNMV IHN+VA  A VGL GR
Sbjct: 476 TGSNTVSDLLFAEFQWGVAAQLELPRQIIVAAQVVGGAMGNMVCIHNIVAVCAVVGLAGR 535

Query: 526 EGSTLRKTIWPTLYYVLFTGVIGLIAIYV 554
           EG  L++T WP + Y L  G+I  +  +V
Sbjct: 536 EGMILKRTFWPFMLYGLVVGIIASLMCFV 564


Lambda     K      H
   0.326    0.140    0.415 

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: 1027
Number of extensions: 60
Number of successful extensions: 6
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: 564
Length of database: 570
Length adjustment: 36
Effective length of query: 528
Effective length of database: 534
Effective search space:   281952
Effective search space used:   281952
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: 53 (25.0 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