Alignments for a candidate for lctP in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Alignments for a candidate for lctP in Desulfovibrio vulgaris Miyazaki F

Align L-lactate permease (characterized, see rationale)
to candidate 8501398 DvMF_2129 L-lactate transport (RefSeq)

Query= uniprot:Q8EIL2
         (545 letters)



>FitnessBrowser__Miya:8501398
          Length = 551

 Score =  574 bits (1480), Expect = e-168
 Identities = 290/550 (52%), Positives = 385/550 (70%), Gaps = 10/550 (1%)

Query: 1   MTWTQTYTPLGSLWLTAIVALLPIVFFFLALTVLKLKGHIAGALTLLIALAVAIITYKMP 60
           M W Q Y PL ++ L+A+VA +P+   F  L V + KGH A AL    A+ +AI+ + MP
Sbjct: 1   MNWVQNYDPLSNILLSALVAAVPLYVLFYMLAVRRAKGHFAAALGTTAAVLLAILVWGMP 60

Query: 61  VSIALASAIYGFSYGLWPIAWIIITAVFLYKITVKTGQFEIIRSSVISVTEDQRLQMLLV 120
           V++A+ + +YG +YGL+PI WI+ITAV++Y +TV++G+FEII+ S+  +T+D+RLQ + +
Sbjct: 61  VNLAVNATLYGAAYGLFPIVWIVITAVWIYNMTVESGEFEIIKDSLARLTDDRRLQAIFI 120

Query: 121 GFSFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAG 180
            F+FG+F+EG AGFG PVAITAA+LVGLGFNPLYAAG+CLIANTAPVAFGA+GIP+IVAG
Sbjct: 121 AFAFGSFIEGTAGFGTPVAITAAMLVGLGFNPLYAAGICLIANTAPVAFGAIGIPVIVAG 180

Query: 181 QVSSLDPFHIGQLAGRQLPILSIIVPFWLIAMMDGIRGIRQTWPATLVAGVSFAVTQFLT 240
           QVS LD  HI Q+ GRQLP LSIIVP WL   M G +   +  PA +VAGV FA +Q+  
Sbjct: 181 QVSGLDTMHISQIVGRQLPFLSIIVPLWLCVTMCGFKRSLEVLPAVIVAGVCFAGSQYAF 240

Query: 241 SNFIGPELPDITSALVSLICLTLFLKVWQPKEIFTFSGMKQRAVTPKSTFSNGQIFKAWS 300
           SNF GP LPDI SA++++I L L L+VW+P   + F      ++T  S +S G+I +AW 
Sbjct: 241 SNFHGPTLPDIMSAIITIIGLVLLLRVWKPATTWHFPDETPSSLTGPSPYSFGEIIRAWM 300

Query: 301 PFIILTAIVTLWSIKDVQ------LALSFATISIE---VPYLHNLVIKTAPIVAKETPYA 351
           P+IIL  +V  W + +++      L   F  ++ +    P LHN + KTAPIVA   PY 
Sbjct: 301 PYIILAIMVFFWGLPEIKPYLDGALGAGFTPLAAKGFAWPGLHNAIEKTAPIVAANAPYG 360

Query: 352 AIYKLNLLGAVGTAILIAAMISIVVL-KMSISNALTSFKDTLIELRFPILSIGLVLAFAF 410
           A++KLN++ A GTAIL   + ++ ++ K     A+     T+ +LRFPIL+I ++L  A 
Sbjct: 361 AMFKLNIISAAGTAILFTGLAAVPMMPKYGYGQAIPCLFRTMHQLRFPILTIAMILGLAQ 420

Query: 411 VANYSGLSSTLALVLAGTGVAFPFFSPFLGWLGVFLTGSDTSSNALFGALQANTANQIGV 470
           + NYSG+SST+ L    TG  FPFFSP LGWLGVFLTGSDTSSNALF  LQ  TA  +G+
Sbjct: 421 IMNYSGMSSTMGLAFTKTGWLFPFFSPLLGWLGVFLTGSDTSSNALFSGLQRTTATSVGM 480

Query: 471 TPELLVAANTTGGVTGKMISPQSIAVACAATGLAGKESDLFRFTLKHSLFFCTFIGVLTV 530
            P L VAAN++GGVTGKMISPQSI+VA AAT + G+E  LFRFTL HS+    FI VLT+
Sbjct: 481 DPHLAVAANSSGGVTGKMISPQSISVATAATKMVGQEGQLFRFTLWHSVAMTAFICVLTM 540

Query: 531 LQAYIVPWTL 540
           LQAY + W L
Sbjct: 541 LQAYPLKWML 550


Lambda     K      H
   0.327    0.140    0.419 

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: 977
Number of extensions: 32
Number of successful extensions: 4
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: 545
Length of database: 551
Length adjustment: 36
Effective length of query: 509
Effective length of database: 515
Effective search space:   262135
Effective search space used:   262135
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
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