GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lctP in Pseudomonas fluorescens FW300-N1B4

Align L-lactate and D-lactate permease (lctP family) (characterized)
to candidate Pf1N1B4_4246 L-lactate permease

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



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4246 L-lactate permease
          Length = 585

 Score =  479 bits (1232), Expect = e-139
 Identities = 255/576 (44%), Positives = 357/576 (61%), Gaps = 28/576 (4%)

Query: 4   WQQLYSPLGSLGLSALAAVIPIVFFFLALAVFRLKGHVAGSITLALAIAVAIFAFNMPAD 63
           WQQ+Y P  +  LS + A +P+V    +LA F +K H+A  + L  A+ +AIFAF MPA+
Sbjct: 3   WQQIYDPFDNPMLSTIMAAVPVVVMLASLAFFHIKAHLAALLALGSALLIAIFAFGMPAN 62

Query: 64  MAFAAAGYGFAYGLWPIAWIIVAAVFLYKLTVKSGQFEVIRSSVLSITDDQRLQVLLIGF 123
           MA +AA YG A GL PI WI++  +FL++LT ++G F+V++ S+  ITDD+RLQ+LLI F
Sbjct: 63  MAGSAALYGAANGLLPIGWIVLNIIFLHRLTTENGSFKVLQDSLARITDDRRLQLLLIAF 122

Query: 124 CFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGALGIPIIVAGQV 183
           CFGAF EGAAGFG PVA+T A+L+GLGF+PL A+GL LIANTAPVAFGALG PII   +V
Sbjct: 123 CFGAFFEGAAGFGTPVAVTGAILIGLGFSPLAASGLALIANTAPVAFGALGTPIITLAKV 182

Query: 184 TGIDAFKIGAMTGRQLPLLSLFVPFWLVFMMDGLRGVRETWPAALVAGLSFAITQYFTSN 243
           TG+D  ++  M GRQLP  S+ VPFWL++   G R + E WPA L+AG+SFA+ Q+  SN
Sbjct: 183 TGLDEMELSMMVGRQLPFFSVIVPFWLIWAFAGWRKMLEIWPAILIAGVSFAVPQFLVSN 242

Query: 244 FIGPELPDITSALASLISLTLFLKVWQPKRT-AGAQIAGATSSATVTASVGGFGQPRSTV 302
           + GP L D+ +AL S+  LT FLKVW+P      A ++G   ++ V   V    +P +T 
Sbjct: 243 YHGPMLVDVIAALISMACLTGFLKVWKPATVHTSAALSGRADNSRV--DVDPDEEPSATF 300

Query: 303 ASPYSLGEIIKAWSPFLILTVLVTIWTLKPFKAMF----------------------AAG 340
           AS  +   +++AW P++ILTV V  W  + FK +F                         
Sbjct: 301 ASD-AKPAVMRAWMPWIILTVFVFAWGTQSFKNLFDTRPVMDPQTHSAKLDPQGKPMREA 359

Query: 341 GSMYGWVFNFAIPHLDQMVIKVAPIVINPTAIPAVFKLDPISATGTAIFFSALISMLVLK 400
             ++     F   H  Q + KV P+V       A++K +  ++TG+ I  +AL+  L++ 
Sbjct: 360 NPIFAPTLTFTTIH--QQIEKVPPVVPVAKTEDAIYKFNWFTSTGSGILLAALLGGLLMG 417

Query: 401 INIKTGLTTFKETLFELRWPILSIGMVLAFAFVTNYSGMSSTMALVLAGTGAAFPFFSPF 460
            +I   L  +  TL+ +R+ +++I  +LA  F+T YSG+ +TM L  A TG  +P F   
Sbjct: 418 YSIPQLLHHYLRTLWVVRYSLITIVAMLALGFLTRYSGLDATMGLAFAATGIFYPMFGTL 477

Query: 461 LGWLGVFLTGSDTSSNALFSSLQATTAHQIGVNDTLLVAANTSGGVTGKMISPQSIAVAC 520
           LGWLGV LTGSDT+SN LF  LQ  TA Q+G++  L+ AAN+SGGV GKM+  QSI VA 
Sbjct: 478 LGWLGVALTGSDTASNVLFGGLQRVTAEQLGLSPVLMAAANSSGGVMGKMVDAQSIVVAS 537

Query: 521 AATGLVGKESDLFRFTLKHSLFFATIVGLITLAQAY 556
            AT   G E ++ R+   HS+  A +VG +   QAY
Sbjct: 538 TATRWYGHEGEILRYVFFHSVVLAILVGGLVTLQAY 573


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: 867
Number of extensions: 35
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: 585
Length adjustment: 36
Effective length of query: 528
Effective length of database: 549
Effective search space:   289872
Effective search space used:   289872
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