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)
to candidate 8499614 DvMF_0381 L-lactate transport (RefSeq)

Query= SwissProt::P71067
         (563 letters)



>FitnessBrowser__Miya:8499614
          Length = 506

 Score =  295 bits (756), Expect = 2e-84
 Identities = 188/542 (34%), Positives = 291/542 (53%), Gaps = 54/542 (9%)

Query: 16  LSALAALVPIIFFFWALAIKRMKGYTAGLATLGIALIIAVLVY-RMPAEKALMSATQGAV 74
           L   AAL PI++  ++L + ++  Y     TL   L +AV  + +MPA  AL +A +GA 
Sbjct: 7   LQLAAALAPIVWLIFSLVVLKLPAYRTCALTLVCTLALAVFGWWKMPAFMALSAALEGAA 66

Query: 75  YGLLPIGWIIVTSVFLYKITVKTGQFDIIRSSVLSITDDRRLQALLIAFSFGAFLEGAAG 134
             L PI  +I+ +VF Y +   TG  D+I   + SIT D+RL  L++A+ FG FLEG AG
Sbjct: 67  MALWPIMIVIIAAVFTYNLARHTGSMDVITRMLSSITTDKRLLVLIVAWGFGGFLEGVAG 126

Query: 135 FGAPVAISAALLVGLGFNPLYAAGICLIANTAPVAFGAIGIPITAVEGPTGIPAMEISQM 194
           +G  VAI A++L  +GF P++AA ICL+ANT P AFGAIGIPI  + G TG+P   IS  
Sbjct: 127 YGTAVAIPASILAAMGFQPMFAAVICLVANTVPTAFGAIGIPIVTMAGVTGLPVETISYY 186

Query: 195 VGRQLPFLSVFIPLYLIIIMSGFRKALEIWPAILVSGVSFAVVQYLSSNFLGPELPDVLS 254
              QL    + I   L+I+ +GF+    ++ A LVSG++FA  Q  ++ ++G ELP ++ 
Sbjct: 187 TALQLFVFIILITYLLVILTAGFKGIKGVFWATLVSGLAFAFPQLYTAKYMGAELPCLIG 246

Query: 255 ALVSMAALAVFLKWWKPKTTFRFAGEQESAASIETARTNPAAPAYRGGQIFKAWSPFLLL 314
           ++ SM A  V+ + +           +++AA ++     PAA      +  KAW P++L+
Sbjct: 247 SVCSMIATIVWARLF----------HRDTAAQVDPI---PAA------EKVKAWLPYILV 287

Query: 315 TAMISVWG--IPSVKSALTGHYEGSAVFLKWLNAVGEKLTFSPGVPFLNNQIVNADGTPI 372
            A I +     P+++ A              L +V   +      PF             
Sbjct: 288 FAFIILCSNLFPAIRDA--------------LGSVKTTVRIYGDNPF------------- 320

Query: 373 EAVYKLEVLGSAGTAILIAAVLSKFITAISWKDWGTVFKETVQELKLPILTIASVVGFAY 432
                 + + + G  I+IA  +   I  +  ++   V   T ++L    +T+ S+V  A 
Sbjct: 321 ----TFKWIATPGALIIIATYIGGMIQGVKVREITGVLGSTAKKLVYSGVTVVSIVALAK 376

Query: 433 VTNSSGMSTTLGMTLA-LTGSMFTFFSPVLGWLGVFITGSDTSANLLFGNLQKVTALSVG 491
           V ++SGM  T+ + +A  T S F F SP+LG LG F+TGSDTS+N+LFG LQ   A  + 
Sbjct: 377 VMSTSGMINTIAIAVADSTSSYFPFISPLLGALGTFVTGSDTSSNVLFGQLQMEVANRIS 436

Query: 492 MDPVLSVAANSSGGVTGKMISPQSIAVACAAVGLAGKESDLFRFTIKHSLFLLLLVCIIT 551
           +D    V+A+++G   GKMISPQSIAVA AA GL G E  +   T+   +  +L++  + 
Sbjct: 437 IDSTWIVSASAAGATAGKMISPQSIAVATAATGLTGYEGRIMNRTLAVCVGYVLVLGTLV 496

Query: 552 FL 553
           ++
Sbjct: 497 YV 498


Lambda     K      H
   0.325    0.138    0.414 

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: 768
Number of extensions: 33
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: 563
Length of database: 506
Length adjustment: 35
Effective length of query: 528
Effective length of database: 471
Effective search space:   248688
Effective search space used:   248688
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: 52 (24.6 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:

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