Aligments for a candidate for lctP in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Aligments for a candidate for lctP in Shewanella oneidensis MR-1

Align L-lactate and D-lactate permease (lctP family) (characterized)
to candidate 200013 SO0827 L-lactate permease (NCBI ptt file)

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



>lcl|FitnessBrowser__MR1:200013 SO0827 L-lactate permease (NCBI ptt
           file)
          Length = 545

 Score =  753 bits (1945), Expect = 0.0
 Identities = 376/554 (67%), Positives = 450/554 (81%), Gaps = 21/554 (3%)

Query: 3   TWQQLYSPLGSLGLSALAAVIPIVFFFLALAVFRLKGHVAGSITLALAIAVAIFAFNMPA 62
           TW Q Y+PLGSL L+A+ A++PIVFFFLAL V +LKGH+AG++TL +A+AVAI  + MP 
Sbjct: 2   TWTQTYTPLGSLWLTAIVALLPIVFFFLALTVLKLKGHIAGALTLLIALAVAIITYKMPV 61

Query: 63  DMAFAAAGYGFAYGLWPIAWIIVAAVFLYKLTVKSGQFEVIRSSVLSITDDQRLQVLLIG 122
            +A A+A YGF+YGLWPIAWII+ AVFLYK+TVK+GQFE+IRSSV+S+T+DQRLQ+LL+G
Sbjct: 62  SIALASAIYGFSYGLWPIAWIIITAVFLYKITVKTGQFEIIRSSVISVTEDQRLQMLLVG 121

Query: 123 FCFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGALGIPIIVAGQ 182
           F FGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGA+GIPIIVAGQ
Sbjct: 122 FSFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAGQ 181

Query: 183 VTGIDAFKIGAMTGRQLPLLSLFVPFWLVFMMDGLRGVRETWPAALVAGLSFAITQYFTS 242
           V+ +D F IG + GRQLP+LS+ VPFWL+ MMDG+RG+R+TWPA LVAG+SFA+TQ+ TS
Sbjct: 182 VSSLDPFHIGQLAGRQLPILSIIVPFWLIAMMDGIRGIRQTWPATLVAGVSFAVTQFLTS 241

Query: 243 NFIGPELPDITSALASLISLTLFLKVWQPKRTAGAQIAGATSSATVTASVGGFGQPRSTV 302
           NFIGPELPDITSAL SLI LTLFLKVWQPK                  +  G  Q   T 
Sbjct: 242 NFIGPELPDITSALVSLICLTLFLKVWQPKE---------------IFTFSGMKQRAVTP 286

Query: 303 ASPYSLGEIIKAWSPFLILTVLVTIWTLKPFKAMFAAGGSMYGWVFNFAIPHLDQMVIKV 362
            S +S G+I KAWSPF+ILT +VT+W++K  +   +          +  +P+L  +VIK 
Sbjct: 287 KSTFSNGQIFKAWSPFIILTAIVTLWSIKDVQLALSFA------TISIEVPYLHNLVIKT 340

Query: 363 APIVINPTAIPAVFKLDPISATGTAIFFSALISMLVLKINIKTGLTTFKETLFELRWPIL 422
           APIV   T   A++KL+ + A GTAI  +A+IS++VLK++I   LT+FK+TL ELR+PIL
Sbjct: 341 APIVAKETPYAAIYKLNLLGAVGTAILIAAMISIVVLKMSISNALTSFKDTLIELRFPIL 400

Query: 423 SIGMVLAFAFVTNYSGMSSTMALVLAGTGAAFPFFSPFLGWLGVFLTGSDTSSNALFSSL 482
           SIG+VLAFAFV NYSG+SST+ALVLAGTG AFPFFSPFLGWLGVFLTGSDTSSNALF +L
Sbjct: 401 SIGLVLAFAFVANYSGLSSTLALVLAGTGVAFPFFSPFLGWLGVFLTGSDTSSNALFGAL 460

Query: 483 QATTAHQIGVNDTLLVAANTSGGVTGKMISPQSIAVACAATGLVGKESDLFRFTLKHSLF 542
           QA TA+QIGV   LLVAANT+GGVTGKMISPQSIAVACAATGL GKESDLFRFTLKHSLF
Sbjct: 461 QANTANQIGVTPELLVAANTTGGVTGKMISPQSIAVACAATGLAGKESDLFRFTLKHSLF 520

Query: 543 FATIVGLITLAQAY 556
           F T +G++T+ QAY
Sbjct: 521 FCTFIGVLTVLQAY 534


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: 958
Number of extensions: 36
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: 564
Length of database: 545
Length adjustment: 36
Effective length of query: 528
Effective length of database: 509
Effective search space:   268752
Effective search space used:   268752
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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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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, or view the source code.

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