GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lctP in Cupriavidus basilensis 4G11

Align L-lactate permease (characterized, see rationale)
to candidate RR42_RS14610 RR42_RS14610 lactate permease

Query= uniprot:Q8EIL2
         (545 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS14610 RR42_RS14610 lactate
           permease
          Length = 558

 Score =  483 bits (1243), Expect = e-141
 Identities = 246/552 (44%), Positives = 350/552 (63%), Gaps = 15/552 (2%)

Query: 3   WTQTYTPLGSLWLTAIVALLPIVFFFLALTVLKLKGHIAGALTLLIALAVAIITYKMPVS 62
           WTQ Y PLGSL L+ + A +P+     AL    L+ H+A  L L++ + +A   + MP +
Sbjct: 2   WTQVYDPLGSLALSTLAAGIPVAVLLAALAFFHLQAHLAAGLALVVGVVIASAVFGMPAA 61

Query: 63  IALASAIYGFSYGLWPIAWIIITAVFLYKITVKTGQFEIIRSSVISVTEDQRLQMLLVGF 122
           +A  +A  G + GL+PI WI++  +FL+++T   G F+++++S+  +TED+RLQ+LLV F
Sbjct: 62  MAGKAAGLGIASGLFPIGWIVLNIIFLHRLTTINGSFKVLQNSISGITEDRRLQLLLVAF 121

Query: 123 SFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAGQV 182
           SFGAF EGAAGFG PVA+T A+L+GLGF+PL A+GL LIANTAPVAFGA+G P+I    V
Sbjct: 122 SFGAFFEGAAGFGTPVAVTGAILIGLGFSPLAASGLALIANTAPVAFGALGAPLIGLSAV 181

Query: 183 SSLDPFHIGQLAGRQLPILSIIVPFWLIAMMDGIRGIRQTWPATLVAGVSFAVTQFLTSN 242
           + LD  H+  + GRQLP  S++VPFWLI    G+RG+   WPA LVAGV+FAV QFL SN
Sbjct: 182 TGLDLLHLSAMVGRQLPFFSLLVPFWLIWAFAGLRGMLAIWPAILVAGVTFAVPQFLVSN 241

Query: 243 FIGPELPDITSALVSLICLTLFLKVWQPKEIFTFSGMKQR-------------AVTPKST 289
           + GP L D+ +ALVS+ CLTLFLKVW+PKEI+T + +  R             A    S 
Sbjct: 242 YHGPWLVDVIAALVSMGCLTLFLKVWKPKEIWTSTRILGRRDDSKVDDPEAVAAEARASA 301

Query: 290 FSNG-QIFKAWSPFIILTAIVTLWSIKDV-QLALSFATISIEVPYLHNLVIKTAPIVAKE 347
            S G  + KAW P++ILT  V +W + +  +L          +P L   V K  P+V K 
Sbjct: 302 ASAGISVVKAWMPWVILTVFVFVWGVPEFKKLMDGLWQWKFPIPGLDKAVFKVPPVVPKA 361

Query: 348 TPYAAIYKLNLLGAVGTAILIAAMISIVVLKMSISNALTSFKDTLIELRFPILSIGLVLA 407
           T   A++  N+L   GT IL++ ++  +++  S+   +  + +T+  +++ +L+I  +  
Sbjct: 362 TAEGAVFTFNVLSMAGTGILVSGILGGLLMGYSLPRLVREYWETIKLVKYSLLTICAMFG 421

Query: 408 FAFVANYSGLSSTLALVLAGTGVAFPFFSPFLGWLGVFLTGSDTSSNALFGALQANTANQ 467
             ++  YSGL +TL L  A TGV +P F   LGWLGV LTGSDT+SN LFG LQ  TA Q
Sbjct: 422 VGYLTRYSGLDATLGLAFAHTGVLYPLFGTMLGWLGVALTGSDTASNVLFGGLQKTTAEQ 481

Query: 468 IGVTPELLVAANTTGGVTGKMISPQSIAVACAATGLAGKESDLFRFTLKHSLFFCTFIGV 527
           +G++P L+ +AN++GGV GKMI  QSI VA  AT   G E ++ R+   HS+     +G+
Sbjct: 482 LGLSPILMASANSSGGVMGKMIDAQSIVVASTATKWYGHEGEILRYVFFHSIALAILVGL 541

Query: 528 LTVLQAYIVPWT 539
              LQAY+ P+T
Sbjct: 542 FITLQAYVHPFT 553


Lambda     K      H
   0.327    0.140    0.419 

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: 948
Number of extensions: 46
Number of successful extensions: 4
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: 545
Length of database: 558
Length adjustment: 36
Effective length of query: 509
Effective length of database: 522
Effective search space:   265698
Effective search space used:   265698
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, the preprint 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