GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lctP in Cupriavidus basilensis 4G11

Align L-lactate and D-lactate permease (lctP family) (characterized)
to candidate RR42_RS21280 RR42_RS21280 L-lactate permease

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



>lcl|FitnessBrowser__Cup4G11:RR42_RS21280 RR42_RS21280 L-lactate
           permease
          Length = 580

 Score =  822 bits (2124), Expect = 0.0
 Identities = 422/580 (72%), Positives = 477/580 (82%), Gaps = 16/580 (2%)

Query: 1   MQTWQQLYSPLGSLGLSALAAVIPIVFFFLALAVFRLKGHVAGSITLALAIAVAIFAFNM 60
           MQ W Q Y+PLGSL LSALAA +PI+FFFLALAV R+KGHVA +ITL LA+ VAIFA+ M
Sbjct: 1   MQPWTQTYTPLGSLWLSALAAALPILFFFLALAVLRMKGHVAAAITLLLALGVAIFAYGM 60

Query: 61  PADMAFAAAGYGFAYGLWPIAWIIVAAVFLYKLTVKSGQFEVIRSSVLSITDDQRLQVLL 120
           P   A AAAG+GFAYGLWPIAWIIV AVFLYK+ VK+GQF++IR+SVL+ITDDQRLQ+LL
Sbjct: 61  PVPQALAAAGFGFAYGLWPIAWIIVTAVFLYKIVVKTGQFDIIRASVLAITDDQRLQMLL 120

Query: 121 IGFCFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGALGIPIIVA 180
           IGF FGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGA+GIPIIVA
Sbjct: 121 IGFAFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVA 180

Query: 181 GQVTGIDAFKIGAMTGRQLPLLSLFVPFWLVFMMDGLRGVRETWPAALVAGLSFAITQYF 240
           GQVTGIDA  IGAM GRQLPLLSL VPFWLVF+MDG RGV+ETWPAALV G SF++TQYF
Sbjct: 181 GQVTGIDAMHIGAMAGRQLPLLSLAVPFWLVFIMDGKRGVKETWPAALVTGASFSVTQYF 240

Query: 241 TSNFIGPELPDITSALASLISLTLFLKVWQPK----RTAGAQIAGATSSATVTASVG--- 293
           TSN IGPELPDITSAL SL+SLTLFLKVWQPK    R  GA  AG  ++A      G   
Sbjct: 241 TSNHIGPELPDITSALVSLVSLTLFLKVWQPKSASQRAGGAVKAGGGAAALARMGGGLAS 300

Query: 294 ---------GFGQPRSTVASPYSLGEIIKAWSPFLILTVLVTIWTLKPFKAMFAAGGSMY 344
                    G G   +  ASPY++ + ++AW+PF ILT +VT+W+L  FKA+F   G++ 
Sbjct: 301 DAGSFGNGAGDGAGNNRRASPYTVAQTVRAWAPFGILTAIVTVWSLPSFKALFVGNGALA 360

Query: 345 GWVFNFAIPHLDQMVIKVAPIVINPTAIPAVFKLDPISATGTAIFFSALISMLVLKINIK 404
           GWV  F +P LDQ+VIK APIV  P A  AVFKLD +SA GTAI  +ALIS ++L++   
Sbjct: 361 GWVLKFHVPALDQLVIKAAPIVAQPKAYEAVFKLDLVSAVGTAILLTALISAVLLRMKPG 420

Query: 405 TGLTTFKETLFELRWPILSIGMVLAFAFVTNYSGMSSTMALVLAGTGAAFPFFSPFLGWL 464
             L TF ETL ELR PILSIG+VL FAFV NYSGMSST+AL+LAGTGAAFPFFSPFLGWL
Sbjct: 421 AALATFGETLMELRRPILSIGLVLGFAFVANYSGMSSTLALLLAGTGAAFPFFSPFLGWL 480

Query: 465 GVFLTGSDTSSNALFSSLQATTAHQIGVNDTLLVAANTSGGVTGKMISPQSIAVACAATG 524
           GVFLTGSDTSSNALF SLQ+TTAHQIGV+DTLLVAANT+GGVTGKMISPQSIAVACAATG
Sbjct: 481 GVFLTGSDTSSNALFCSLQSTTAHQIGVSDTLLVAANTTGGVTGKMISPQSIAVACAATG 540

Query: 525 LVGKESDLFRFTLKHSLFFATIVGLITLAQAYWFTGMLVH 564
           LVGKES+LFRFT+KHSL FA IVG+IT+ QAY  TGM+ H
Sbjct: 541 LVGKESELFRFTVKHSLLFAMIVGIITMLQAYVLTGMIPH 580


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: 961
Number of extensions: 36
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: 580
Length adjustment: 36
Effective length of query: 528
Effective length of database: 544
Effective search space:   287232
Effective search space used:   287232
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 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