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:A0KZB2
         (547 letters)



>MicrobesOnline__882:208540
          Length = 570

 Score =  390 bits (1002), Expect = e-113
 Identities = 219/564 (38%), Positives = 334/564 (59%), Gaps = 32/564 (5%)

Query: 4   LQLLASLTPVISVMIFLVLLRMPASKAMPISMIITALAAVFIWQMDTTLLAASVLEGLLS 63
           L  L +L P++  ++ +V +R PA+KAMP+S ++  L A+ +W +    + A  L+G+++
Sbjct: 5   LLALVALLPILVALVLMVGMRWPATKAMPLSWLVCVLGAIGVWNLPAGYVTALTLQGIVT 64

Query: 64  AITPLTIIFGAVFLLNTLKYSGAMDTIRAGFTNISADARVQVIIICWLFGAFIEGSAGFG 123
           AI  L I+FGA+ +L TL+YSG M+TI+ G  N+S D R+Q III ++F AFIEG+AGFG
Sbjct: 65  AIGVLIIVFGAIIILYTLQYSGGMETIQYGMQNVSRDKRIQAIIIGYMFAAFIEGAAGFG 124

Query: 124 TPAAIGAPLLVLLGVPPVAAAVVALIADSACVSFGAIGLPVLFGM-------EQGLTQGG 176
           TPAA+ APLL+ LG PP+AAAV+ L+ +S CVSFGA+G P+L G+       +  +T G 
Sbjct: 125 TPAALAAPLLLSLGFPPLAAAVICLVFNSFCVSFGAVGTPILIGLKFLAPLVKDAVTAGT 184

Query: 177 VSLAAEQFAAHGGSYVGYARFIVMHMITIDLITGTLIPLVMVTILTGFFGRNKSFKEGLA 236
             L    F +       +A   +MH   I      ++P+ M+  LT F+G+NKS+ EG  
Sbjct: 185 PGLNFTDFGSFAKVIGQWA--TIMHGFMI-----VILPIFMLGFLTRFYGQNKSWSEGFK 237

Query: 237 IWKFAIFAGLAFTVPAWIINYLAGPEFPSVIGSLVGMALVIPVARKGYLLPKTPWNDFAE 296
            WKF +FA ++F VP +I  +  GPEFPS+IG LVG+ +++  A++G+ +P+  W DF  
Sbjct: 238 AWKFCVFAAVSFAVPYFIFAWFVGPEFPSLIGGLVGLGIIVAGAKRGFCVPEETW-DFGP 296

Query: 297 NDS---------QEGAKIETTAKFSQIAAWTPYIIMAALLVLSRTVA-PLKAWLSSFNIS 346
             +         +  AK E  A  SQ  AW PYI++ A+LV++R  +  LK +LS+  I 
Sbjct: 297 QSTWDPEWTGTIKTAAKTEFKAHMSQFKAWLPYILIGAILVVTRVPSLGLKGFLSAQKIP 356

Query: 347 WTGLMGTE-LKASFATLYAPGAF-FVAVCILGFFLFKMKSPAIKQSIGVSCKSMLPTIIS 404
           +  ++G + + AS   LY PG   F  V +L   L  M   A+K++   S   M    I+
Sbjct: 357 FDNILGFKGVSASIDYLYLPGTIPFTLVALLTILLHGMSGDAVKRAWSESFAKMKAPTIA 416

Query: 405 LGASVPMVKIFLNSGV-----NGAGLASMPVALADMLGQSMGAVWAWMAPIVGIFGAFLS 459
           L  +V +V IF  SGV     N     SMP+A+A  +    G  W  +A  VG  GAF++
Sbjct: 417 LFFAVALVSIFRGSGVADVALNPNNYPSMPLAMAKAVAALAGNAWPMLASYVGGLGAFIT 476

Query: 460 GSATFSNMMFSSLQYSVADNIGMNHTLVLALQGIGANAGNMMCVMNVVAAATVVGMAGRE 519
           GS T S+++F+  Q+ VA  + +   +++A Q +G   GNM+C+ N+VA   VVG+AGRE
Sbjct: 477 GSNTVSDLLFAEFQWGVAAQLELPRQIIVAAQVVGGAMGNMVCIHNIVAVCAVVGLAGRE 536

Query: 520 SEIIRKTMPVAIGYALLAGTIATL 543
             I+++T    + Y L+ G IA+L
Sbjct: 537 GMILKRTFWPFMLYGLVVGIIASL 560


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: 945
Number of extensions: 57
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: 570
Length adjustment: 36
Effective length of query: 511
Effective length of database: 534
Effective search space:   272874
Effective search space used:   272874
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