Aligments for a candidate for lctP in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Aligments for a candidate for lctP in Desulfovibrio vulgaris Miyazaki F

Align L-lactate permease (characterized, see rationale)
to candidate 8501125 DvMF_1861 L-lactate permease (RefSeq)

Query= uniprot:A0KZB2
         (547 letters)



>FitnessBrowser__Miya:8501125
          Length = 569

 Score =  383 bits (984), Expect = e-111
 Identities = 220/562 (39%), Positives = 333/562 (59%), Gaps = 29/562 (5%)

Query: 4   LQLLASLTPVISVMIFLVLLRMPASKAMPISMIITALAAVFIWQMDTTLLAASVLEGLLS 63
           L  L +L P++  ++ +V +R P+++AMP++ ++  L A+  W +    +AA  L+G+++
Sbjct: 5   LLALVALLPILVALVLMVGMRWPSTRAMPLAWLVCVLGAIGAWNLPAGYIAALSLQGVVT 64

Query: 64  AITPLTIIFGAVFLLNTLKYSGAMDTIRAGFTNISADARVQVIIICWLFGAFIEGSAGFG 123
           AI  L I+FGA+ +L TLKYSG M+TI+ G  NIS D R+Q III ++F AFIEG+AGFG
Sbjct: 65  AIGVLIIVFGAIIILYTLKYSGGMETIQYGMQNISRDKRIQAIIIGYMFAAFIEGAAGFG 124

Query: 124 TPAAIGAPLLVLLGVPPVAAAVVALIADSACVSFGAIGLPVLFGMEQGLTQGGVSLAAEQ 183
           TPAA+ APLL+ LG PP+AAAV+ L+ +S CVSFGA+G P+L G+     +    L  + 
Sbjct: 125 TPAALAAPLLLSLGFPPLAAAVICLVFNSFCVSFGAVGTPILIGL-----KFLAPLVKDA 179

Query: 184 FAAHGG-SYVGYARFIVMHMITIDLITGTLI---PLVMVTILTGFFGRNKSFKEGLAIWK 239
            AA+ G ++  +  F  +    + L+ G +I   P+ M+  LT F+G+ KS+ EG A W+
Sbjct: 180 AAANPGLNFTDFGSFAKVIGQWVTLMHGPMIFILPIFMLGFLTRFYGQKKSWAEGFAAWQ 239

Query: 240 FAIFAGLAFTVPAWIINYLAGPEFPSVIGSLVGMALVIPVARKGYLLPKTPWNDFAENDS 299
           F +FA +AF VP     +L GPEFPS+IG LVG+ +++  A+KG+ +PK  W DF    +
Sbjct: 240 FCVFAAVAFIVPYLTFAWLVGPEFPSLIGGLVGLGIIVAGAKKGFCVPKETW-DFGPQST 298

Query: 300 QEGAKIETTA---------KFSQIAAWTPYIIMAALLVLSR-TVAPLKAWLSSFNISWTG 349
            E     T A           SQ  AW PYI++  +LVL+R     LK W+S+  +    
Sbjct: 299 WEAEWTGTIATSTNTEFKPHMSQFMAWLPYILIGVILVLTRIPELGLKGWMSAQKLPIND 358

Query: 350 LMGTE-LKASFATLYAPGAF-FVAVCILGFFLFKMKSPAIKQSIGVSCKSMLPTIISLGA 407
           ++G + + AS   LY PG   F  V +L   L  MK  A+K++   S   M    I+L A
Sbjct: 359 ILGYKGVSASIDYLYLPGTIPFTLVALLTIMLHGMKGDAVKKAWSESFSKMKAPTIALFA 418

Query: 408 SVPMVKIFLNSGVNGAGL-----ASMPVALADMLGQSMGAVWAWMAPIVGIFGAFLSGSA 462
           +V +V IF  SGV  A L      SMP+A+A  +    G  W  +A  VG  GAF++GS 
Sbjct: 419 AVALVSIFRGSGVADAALNPNNYPSMPLAMAKTVAAFAGNAWPMLASYVGGLGAFITGSN 478

Query: 463 TFSNMMFSSLQYSVADNIGMNHTLVLALQGIGANAGNMMCVMNVVAAATVVGMAGRESEI 522
           T S+++F+  Q+ VA  + +   +++A Q  G   GNM+C+ N+VA   V G+ GRE  I
Sbjct: 479 TVSDLLFAEFQWGVAQQLSLPRQIIVAAQVAGGAMGNMVCIHNIVAVCAVTGLIGREGMI 538

Query: 523 IRKTM-PVAIGYALLAGTIATL 543
           +++T  P A+ Y ++ G IA++
Sbjct: 539 LKRTFWPFAL-YGIVVGIIASI 559


Lambda     K      H
   0.326    0.138    0.413 

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: 970
Number of extensions: 60
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: 547
Length of database: 569
Length adjustment: 36
Effective length of query: 511
Effective length of database: 533
Effective search space:   272363
Effective search space used:   272363
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 paper from 2022 on GapMind for carbon sources, or view the source code.

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