GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Cup4G11:RR42_RS21280
          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 (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