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.

Links

Downloads

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, 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