Alignments for a candidate for lctP in Chromobacterium vaccinii MWU205

GapMind for catabolism of small carbon sources

Alignments for a candidate for lctP in Chromobacterium vaccinii MWU205

Align L-lactate and D-lactate permease (lctP family) (characterized)
to candidate WP_046158450.1 VL52_RS18675 lactate permease LctP family transporter

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



>NCBI__GCF_000971335.1:WP_046158450.1
          Length = 544

 Score =  775 bits (2002), Expect = 0.0
 Identities = 388/553 (70%), Positives = 451/553 (81%), Gaps = 15/553 (2%)

Query: 4   WQQLYSPLGSLGLSALAAVIPIVFFFLALAVFRLKGHVAGSITLALAIAVAIFAFNMPAD 63
           W Q Y P G   LSAL A +PI FFF+ALAV RLKGHVAG++T+ +A+ VAI  + MPA 
Sbjct: 5   WTQQYFPAGGPALSALMAALPIAFFFVALAVLRLKGHVAGTLTVLIALVVAILFYGMPAQ 64

Query: 64  MAFAAAGYGFAYGLWPIAWIIVAAVFLYKLTVKSGQFEVIRSSVLSITDDQRLQVLLIGF 123
           MA AAA +GF YGLWPIAWIIVAAVFLYK+TVK+GQF++IR+SVLS+T+DQRLQ+LL+GF
Sbjct: 65  MALAAAAFGFGYGLWPIAWIIVAAVFLYKITVKTGQFDIIRASVLSVTEDQRLQMLLVGF 124

Query: 124 CFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGALGIPIIVAGQV 183
            FGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGA+GIPIIVAGQV
Sbjct: 125 SFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAGQV 184

Query: 184 TGIDAFKIGAMTGRQLPLLSLFVPFWLVFMMDGLRGVRETWPAALVAGLSFAITQYFTSN 243
           TG+D F IGA  G QLP+LS+ VPFWLV MMDGL+GVR+TWPA LVAG+SFA+TQ+FTSN
Sbjct: 185 TGLDPFLIGAKAGHQLPILSVIVPFWLVMMMDGLKGVRQTWPAILVAGVSFAVTQFFTSN 244

Query: 244 FIGPELPDITSALASLISLTLFLKVWQPKRTAGAQIAGATSSATVTASVGGFGQPRSTVA 303
           +IGPELPDITSAL SL+ LTLFLK WQP                   +  G   P +  A
Sbjct: 245 YIGPELPDITSALVSLVCLTLFLKTWQPSE---------------IFTFNGRRAPSARQA 289

Query: 304 SPYSLGEIIKAWSPFLILTVLVTIWTLKPFKAMFAAGGSMYGWVFNFAIPHLDQMVIKVA 363
           S +SLG+I +AWSPFLILT LVT+W++KPFKA+F  GG++ GW++   +P LD++V+K A
Sbjct: 290 SGFSLGQIARAWSPFLILTALVTVWSVKPFKALFIKGGALEGWIWKLHVPGLDKLVLKTA 349

Query: 364 PIVINPTAIPAVFKLDPISATGTAIFFSALISMLVLKINIKTGLTTFKETLFELRWPILS 423
           PIV + T   A++K D +SA G+AIF SAL+SM +LK     GL T  ETL ELR PILS
Sbjct: 350 PIVAHETPYEALYKFDIVSAVGSAIFLSALLSMALLKFRPADGLRTLGETLVELRRPILS 409

Query: 424 IGMVLAFAFVTNYSGMSSTMALVLAGTGAAFPFFSPFLGWLGVFLTGSDTSSNALFSSLQ 483
           IGMVLAFAFV NYSGMSST+AL LAGTG AFPFFSPFLGWLGVFLTGSDTSSNALFS+LQ
Sbjct: 410 IGMVLAFAFVANYSGMSSTLALCLAGTGKAFPFFSPFLGWLGVFLTGSDTSSNALFSALQ 469

Query: 484 ATTAHQIGVNDTLLVAANTSGGVTGKMISPQSIAVACAATGLVGKESDLFRFTLKHSLFF 543
           A TAHQ+GV+D LLVAANT+GGVTGKMISPQSIAVACAA GL+G+E+DLFRFTLKHSL F
Sbjct: 470 AATAHQLGVSDVLLVAANTTGGVTGKMISPQSIAVACAAVGLIGREADLFRFTLKHSLIF 529

Query: 544 ATIVGLITLAQAY 556
            + VGL+T   AY
Sbjct: 530 CSFVGLLTWLMAY 542


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: 954
Number of extensions: 32
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: 544
Length adjustment: 36
Effective length of query: 528
Effective length of database: 508
Effective search space:   268224
Effective search space used:   268224
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