Alignments for a candidate for lctP in Desulfovibrio oxyclinae DSM 11498

GapMind for catabolism of small carbon sources

Alignments for a candidate for lctP in Desulfovibrio oxyclinae DSM 11498

Align L-lactate permease (characterized, see rationale)
to candidate WP_018123841.1 B149_RS0103815 L-lactate permease

Query= uniprot:L0GFN1
         (564 letters)



>NCBI__GCF_000375485.1:WP_018123841.1
          Length = 569

 Score =  480 bits (1236), Expect = e-140
 Identities = 255/567 (44%), Positives = 367/567 (64%), Gaps = 17/567 (2%)

Query: 1   MSNGLLALFAFTPILLAAIMLIGLRWPASRAMPLVFLFTAAIGLFVWDMSVNRIIASTLQ 60
           MS  LLAL A  PIL+A ++++G+RWPA++AMP+ +L  AA  +  W +  + + A TLQ
Sbjct: 1   MSLELLALVALLPILVALVLMVGMRWPATKAMPVAWLTCAAGAVLAWQLPASYVAALTLQ 60

Query: 61  GLVITLGLLWIIFGAILLLNTLKHSGGITAIRAGFTTISPDRRIQAIIIAWLFGCFIEGA 120
           G +  +G+L I+FGAI++L TL++SGG+  I+ G   I+ DRRIQAIII ++F  FIEGA
Sbjct: 61  GFITAIGILIIVFGAIIILYTLQYSGGMETIQYGMQNITADRRIQAIIIGYMFAAFIEGA 120

Query: 121 SGFGTPAAIAAPLLVAVGFPAMAAVLLGMLVQSTPVSFGAVGTPIVVG---INSGLDT-- 175
           +GFGTPAA+AAPLL+ +GFP +AA ++ ++  S PV+FGAVGTP+V+G   +N  +D+  
Sbjct: 121 AGFGTPAALAAPLLLTLGFPPLAAAVICLVFNSFPVTFGAVGTPVVLGLKFLNPLVDSAV 180

Query: 176 ATIGAQLVAQGSSWNAYLQQITSSVAITHAIVGTVMPLVMVLMLTRFFGKEKSWKAGFEV 235
           AT+     A    +N  + Q  +   I H  +  ++P+ M+  +TRFFG E+SWK GF  
Sbjct: 181 ATVPGLNFASMGGFNMVVGQWAT---IMHLPMIFILPIFMLGFITRFFGPERSWKPGFGA 237

Query: 236 LPFAIFAGLAFTLPYAATGIFLGPEFPSLLGGLVGLAIVTTAARFKFLTPKTTWDFADAK 295
             F IFA ++FT+PY A    +GPEFPSL+GGLVGL ++   A+  F  P+ +WDF    
Sbjct: 238 WKFCIFAAVSFTIPYLAFAWLVGPEFPSLIGGLVGLGVIVAGAKAGFCMPEKSWDFGPVD 297

Query: 296 EWPAEWLGTIEMKLDEMAARPMSAFRAWLPYVLVGAILVISRVFPQ--VTAALKSVSIAF 353
           +W  EW G+I+          MS FRAWLPY+L+G ILV++R+ P+  +   L S +I F
Sbjct: 298 KWDPEWTGSIKGSDSCEFKCHMSQFRAWLPYMLIGGILVVTRI-PELGLKGFLASQAITF 356

Query: 354 ANILGETGINAGIEPLYLPGGI-LVMVVLITFFLHGMRVSELKAAVKESSGVLLSAGFVL 412
           +NILG   +N  I+ LYLPG I  ++V ++T FLHGMR  ++K A  ES   + +    L
Sbjct: 357 SNILGFESVNGAIKYLYLPGTIPFMLVAVLTIFLHGMRGPDVKKAWGESIAKMKNPAIAL 416

Query: 413 LFTVPMVRILINSGV-----NGAELASMPIVMARYVADSVGSIYPLLAPAVGALGAFLAG 467
            F V +V I   SG+     N     SMP+ MA+ VA+  G+ +P+ A  VG LG+F+ G
Sbjct: 417 FFAVGLVSIFRGSGIADVALNPNNYPSMPLAMAKTVAEITGNAWPMFAAFVGGLGSFITG 476

Query: 468 SNTVSNMMFSQFQFGVAQSLGISGAMVVATQAVGAAAGNMVAIHNVVAASATVGLLGREG 527
           SNTVS+++F++FQ+GVA  L +   ++VA QAVG   GNMV IHN+VA  A VGL G EG
Sbjct: 477 SNTVSDLLFAEFQWGVAAQLDLPRQLIVAAQAVGGGMGNMVCIHNIVAVCAVVGLSGMEG 536

Query: 528 STLRKTIWPTLYYVLFTGVIGLIAIYV 554
           + L+KT+WP L Y L  G++  +  +V
Sbjct: 537 TILKKTVWPLLVYGLVVGLVTTLMSFV 563


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: 1105
Number of extensions: 62
Number of successful extensions: 7
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: 569
Length adjustment: 36
Effective length of query: 528
Effective length of database: 533
Effective search space:   281424
Effective search space used:   281424
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources