GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__MR1:200013
          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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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:

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:

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:

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:

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