Alignments for a candidate for lctP in Alicycliphilus denitrificans K601

GapMind for catabolism of small carbon sources

Alignments for a candidate for lctP in Alicycliphilus denitrificans K601

Align L-lactate and D-lactate permease (lctP family) (characterized)
to candidate WP_013723265.1 ALIDE2_RS22945 L-lactate permease

Query= reanno::pseudo5_N2C3_1:AO356_07550
         (564 letters)



>NCBI__GCF_000204645.1:WP_013723265.1
          Length = 553

 Score =  493 bits (1270), Expect = e-144
 Identities = 264/567 (46%), Positives = 360/567 (63%), Gaps = 22/567 (3%)

Query: 4   WQQLYSPLGSLGLSALAAVIPIVFFFLALAVFRLKGHVAGSITLALAIAVAIFAFNMPAD 63
           WQQ+Y PLG++ +S   A +P+V    AL  F +K H+A  + LA A+ VAIF + MPAD
Sbjct: 3   WQQIYDPLGNMVISTALAAVPVVVMLAALGFFHIKAHIAAGMGLAAALLVAIFVYGMPAD 62

Query: 64  MAFAAAGYGFAYGLWPIAWIIVAAVFLYKLTVKSGQFEVIRSSVLSITDDQRLQVLLIGF 123
           MA  AA  G   GL PI WI++  +FL++LT ++G F V++ S+  IT+D+R+Q+LLI F
Sbjct: 63  MAGRAALLGGFTGLLPIGWIVLNIIFLHQLTEQNGSFAVLQDSLSGITEDRRIQLLLIAF 122

Query: 124 CFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGALGIPIIVAGQV 183
           CFGAF EGAAGFG PVA+TAA+L+GLGF+PL A+GL LIANTAPVAFGALG P+I   +V
Sbjct: 123 CFGAFFEGAAGFGTPVAVTAAILIGLGFSPLAASGLSLIANTAPVAFGALGTPVITLAKV 182

Query: 184 TGIDAFKIGAMTGRQLPLLSLFVPFWLVFMMDGLRGVRETWPAALVAGLSFAITQYFTSN 243
            G D  ++ AM GRQLP  SL VPFWL++   G +G+ E WPA LV G+SFAI Q+  SN
Sbjct: 183 HGYDLMEVTAMIGRQLPFFSLLVPFWLIWAFAGRKGMMEIWPAILVTGVSFAIPQFLVSN 242

Query: 244 FIGPELPDITSALASLISLTLFLKVWQPKRTAGAQIAGATSSATVTASVGGFGQPRSTVA 303
           +IGPEL DI +A+ S++ L  FL+VW+P+          TS++     V       +   
Sbjct: 243 YIGPELVDIIAAIVSMVCLVAFLRVWKPRTV-------WTSASLRHHDVSAAEAKPAKPV 295

Query: 304 SPYSLGEIIKAWSPFLILTVLVTIWTLKPFK----AMFAAGGSMYGWVFNFAIPHLDQMV 359
           + +S   ++ AW+P++IL+V V IW L   K     +FA    M G         L  M+
Sbjct: 296 TRHSTQALVAAWTPWVILSVFVFIWGLPSVKTWLNGVFAPAFPMEG---------LHNMI 346

Query: 360 IKVAPIVINPTAIPAVFKLDPISATGTAIFFSALISMLVLKINIKTGLTTFKETLFELRW 419
            KV P+V  PT   AV+ L+ +SATGT I  SA++S  V+K N    + TF +TL+ +++
Sbjct: 347 EKVPPVVAKPTKEGAVYTLNLLSATGTGILLSAIVSAFVMKYNPVAIVRTFFKTLWLVKY 406

Query: 420 PILSIGMVLAFAFVTNYSGMSSTMALVLAGTGAAFPFFSPFLGWLGVFLTGSDTSSNALF 479
            +L+I ++LA   +T YSG  +T+ L  A TG  +PFF   +GWLGV LTGSDT+SN LF
Sbjct: 407 SLLTIVLMLALGTLTRYSGTDTTLGLAFANTGVLYPFFGTLMGWLGVALTGSDTASNVLF 466

Query: 480 SSLQATTAHQIGVNDTLLVAANTSGGVTGKMISPQSIAVACAATGLVGKESDLFRFTLKH 539
             +Q   A Q+ ++  L+ AAN+SGGV GKMI  QSI VA  AT     E D+ R+   H
Sbjct: 467 GGMQKVAAEQLHLSPNLMGAANSSGGVMGKMIDAQSIVVASTATRWFDHEGDILRYVFFH 526

Query: 540 SLFFATIVGLITLAQAY-W-FTGMLVH 564
           S+  A +VGL    QAY W F+ M+VH
Sbjct: 527 SIALACLVGLYVTMQAYVWPFSLMVVH 553


Lambda     K      H
   0.327    0.139    0.422 

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: 815
Number of extensions: 38
Number of successful extensions: 2
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: 564
Length of database: 553
Length adjustment: 36
Effective length of query: 528
Effective length of database: 517
Effective search space:   272976
Effective search space used:   272976
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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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