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_015944591.1 DHAF_RS17005 lactate permease

Query= TCDB::Q46839
         (560 letters)



>NCBI__GCF_000021925.1:WP_015944591.1
          Length = 554

 Score =  612 bits (1579), Expect = e-180
 Identities = 323/559 (57%), Positives = 397/559 (71%), Gaps = 22/559 (3%)

Query: 4   WTQMYMPMGG-LGLSALVALIPIIFFFVALAVLRLKGHVAGAITLILSILIAIFAFKMPI 62
           WTQ Y  +GG LGL+AL   IPI+F F ALAV  +KG+VAG ITL +SI+  I  +KMP+
Sbjct: 3   WTQDYAALGGSLGLTALAVSIPIVFLFWALAVKGMKGYVAGLITLAISIVDVIIVYKMPV 62

Query: 63  DMAFAAAGYGFIYGLWPIAWIIVAAVFLYKLTVASGQFDIIRSSVISITDDQRLQVLLIG 122
            +A +A  YG +YGLWPIAWI++ AV+LY LTV SGQFDII+SS+ SI+DD+RLQ L++ 
Sbjct: 63  TLALSATAYGMLYGLWPIAWIVITAVYLYNLTVVSGQFDIIKSSIASISDDRRLQALIVA 122

Query: 123 FSFGALLEGAAGFGAPVAITGALLVGLGFKPLYAAGLCLIANTAPVAFGALGVPILVAGQ 182
           F FGA LEGAAGFGAPVAITGALL+GLGF P+ AAGLCLIANTAPVAFGA+G PI+ AG 
Sbjct: 123 FCFGAFLEGAAGFGAPVAITGALLIGLGFDPIKAAGLCLIANTAPVAFGAIGAPIITAGA 182

Query: 183 VTGIDPFHIGAMAGRQLPFLSVLVPFWLVAMMDGWKGVKETWPAALVAGGSFAVTQFFTS 242
           VTG+  F I    GRQLPFLSV++P +LV +M GWK  KE  PA LV G SFAV Q++++
Sbjct: 183 VTGMGDFVISQAVGRQLPFLSVIIPLYLVILMAGWKSAKEVMPAILVTGVSFAVAQWWSA 242

Query: 243 NYIGPELPDITSALVSIVSLALFLKVWRPKNTETAISMGQSAGAMVVNKPSSGG---PVP 299
           NY+G  LPDI S+L S+V   +FL+ W+PK               V   P   G   P  
Sbjct: 243 NYLGAYLPDIISSLFSLVCTTVFLRFWKPKT--------------VWRFPHERGTKEPEM 288

Query: 300 SEYSLGQIIRAWSPFLILTVLVTIWTMKPFKALFAPGGAFYSLVINFQIPHLHQQVLKAA 359
            +Y+ GQI +AWSPF+ILTV+VTIW    FK           LV+ F  P L   + KAA
Sbjct: 289 KKYTGGQIAKAWSPFVILTVMVTIWGTPSFKTFILDK---LHLVLKFSWPGLDGLIYKAA 345

Query: 360 PIVAQPTPMDAVFKFDPLSAGGTAIFIAAIISIFILGVGIKKGIGVFAETLISLKWPILS 419
           PIVA+PT  +A+FK+D LSAGGTAI IAAIIS  ILG+     + VF +TL  L +P+++
Sbjct: 346 PIVAKPTVYEAIFKWDFLSAGGTAILIAAIISTIILGIKPSTAVKVFGDTLKQLMYPVIN 405

Query: 420 IGMVLAFAFVTNYSGMSTTLALVLAGTGVMFPFFSPFLGWLGVFLTGSDTSSNALFGSLQ 479
           I  VL FA++ NYSG+S TL L  A TG  FP  SP LGWLGVFLTGSDTS+NALFG LQ
Sbjct: 406 ISAVLGFAYLANYSGLSYTLGLFFASTGAFFPVLSPVLGWLGVFLTGSDTSANALFGKLQ 465

Query: 480 STTAQQINVSDTLLVAANTSGGVTGKMISPQSIAVACAATGMVGRESELFRYTVKHSLIF 539
             TA+Q+ ++  L VAAN+SGGV GKMISPQSIAVA AAT +VGRESELF++TVKHSL  
Sbjct: 466 QVTAEQLGMNPVLTVAANSSGGVVGKMISPQSIAVA-AATTLVGRESELFKFTVKHSLAM 524

Query: 540 ASVIGIITLLQAYVFTGML 558
            + + +I  LQAYV  GM+
Sbjct: 525 LAAVIVIICLQAYVVPGMI 543


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: 967
Number of extensions: 48
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: 560
Length of database: 554
Length adjustment: 36
Effective length of query: 524
Effective length of database: 518
Effective search space:   271432
Effective search space used:   271432
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.

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