Alignments for a candidate for lctP in Desulfitobacterium hafniense DCB-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for lctP in Desulfitobacterium hafniense DCB-2

Align Glycolate permease, GlcA or YghK (substrates: L-lactate, D-lactate and glycolate) (characterized)
to candidate WP_015944592.1 DHAF_RS17015 lactate permease

Query= TCDB::Q46839
         (560 letters)



>NCBI__GCF_000021925.1:WP_015944592.1
          Length = 552

 Score =  609 bits (1571), Expect = e-179
 Identities = 317/556 (57%), Positives = 399/556 (71%), Gaps = 14/556 (2%)

Query: 4   WTQMYMPMGG-LGLSALVALIPIIFFFVALAVLRLKGHVAGAITLILSILIAIFAFKMPI 62
           WTQ Y  +GG + L+ALV  IPI F   ALA+ R+KGH+AG  TL+++++I +  +KMPI
Sbjct: 3   WTQNYSALGGSIALTALVVSIPIFFLLWALAIKRMKGHIAGMSTLLITLVIVVLVYKMPI 62

Query: 63  DMAFAAAGYGFIYGLWPIAWIIVAAVFLYKLTVASGQFDIIRSSVISITDDQRLQVLLIG 122
            +A +A+ YG +YGLWPI+WI+V AVFLY LTV +GQFD+I+ S+ SI++D+R+Q LL+ 
Sbjct: 63  SIALSASLYGILYGLWPISWIVVTAVFLYNLTVEAGQFDVIKGSISSISNDRRIQALLVA 122

Query: 123 FSFGALLEGAAGFGAPVAITGALLVGLGFKPLYAAGLCLIANTAPVAFGALGVPILVAGQ 182
           F FGA LEGAAGFGAPVAI+ ++L+GLGF PLYAAGLCLIANTAPVAFGA+G PI+ AG 
Sbjct: 123 FCFGAFLEGAAGFGAPVAISASILIGLGFNPLYAAGLCLIANTAPVAFGAIGAPIIAAGA 182

Query: 183 VTGIDPFHIGAMAGRQLPFLSVLVPFWLVAMMDGWKGVKETWPAALVAGGSFAVTQFFTS 242
           VTG+  F I    GRQLPFLSV++P +LV +M GWKG KE  PAALVAG +FAV Q+++S
Sbjct: 183 VTGMGDFVISQAIGRQLPFLSVIIPIYLVVLMSGWKGAKEVLPAALVAGIAFAVAQWWSS 242

Query: 243 NYIGPELPDITSALVSIVSLALFLKVWRPKNTETAISMGQSAGAMVVNKPSSGGPVPSEY 302
           N++G  LPDI S+L S+++L LFL+VW+PKN                 +      V   +
Sbjct: 243 NHLGAYLPDIISSLFSLIALTLFLRVWKPKNN----------WRFPHEEGKEDNVVAQRF 292

Query: 303 SLGQIIRAWSPFLILTVLVTIWTMKPFKALFAPGGAFYSLVINFQIPHLHQQVLKAAPIV 362
           + GQII+AWSPF ILTVLV IW    FK      G + ++      P L   V KAAPIV
Sbjct: 293 TAGQIIKAWSPFAILTVLVGIWGTPGFKTWATNAGLYVNIA---HWPGLDGLVYKAAPIV 349

Query: 363 AQPTPMDAVFKFDPLSAGGTAIFIAAIISIFILGVGIKKGIGVFAETLISLKWPILSIGM 422
           A+PT   A +K+D  SA GTAI I+AIIS+FILGV   +   VF +TL  L + I++I  
Sbjct: 350 AKPTVYAAAYKWDWFSAAGTAILISAIISMFILGVSPGRAWKVFVKTLKQLTFAIINIAS 409

Query: 423 VLAFAFVTNYSGMSTTLALVLAGTGVMFPFFSPFLGWLGVFLTGSDTSSNALFGSLQSTT 482
           VL FA++ NYSG+S TL L+ A TG +FPF SP LGWL VFLTGSDTS+NALFG LQ  T
Sbjct: 410 VLGFAYLANYSGLSYTLGLLFASTGSLFPFLSPVLGWLAVFLTGSDTSANALFGKLQQVT 469

Query: 483 AQQINVSDTLLVAANTSGGVTGKMISPQSIAVACAATGMVGRESELFRYTVKHSLIFASV 542
           A+QI V+  L VAAN+SGGV GKMISPQSIAVA AAT +VGRESEL R+T+KHSLI   V
Sbjct: 470 AEQIGVNPVLTVAANSSGGVVGKMISPQSIAVAAAATSLVGRESELLRFTLKHSLILLLV 529

Query: 543 IGIITLLQAYVFTGML 558
           I I+  LQAYV  GM+
Sbjct: 530 ICIMITLQAYVVPGMI 545


Lambda     K      H
   0.327    0.141    0.424 

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: 955
Number of extensions: 37
Number of successful extensions: 3
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: 560
Length of database: 552
Length adjustment: 36
Effective length of query: 524
Effective length of database: 516
Effective search space:   270384
Effective search space used:   270384
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 24 2021. 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 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