GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lctP in Pseudomonas fluorescens FW300-N2E3

Align Glycolate permease, GlcA or YghK (substrates: L-lactate, D-lactate and glycolate) (characterized)
to candidate AO353_23340 AO353_23340 lactate permease

Query= TCDB::Q46839
         (560 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_23340
          Length = 587

 Score =  497 bits (1280), Expect = e-145
 Identities = 258/578 (44%), Positives = 357/578 (61%), Gaps = 28/578 (4%)

Query: 2   VTWTQMYMPMGGLGLSALVALIPIIFFFVALAVLRLKGHVAGAITLILSILIAIFAFKMP 61
           + W Q+Y P G   +S L+A +P++    +LA   LK H+A  + L  ++LIAIFAF MP
Sbjct: 1   MVWQQVYDPFGNPLVSTLMAALPVVVMLTSLAFFHLKAHIAALLALSTALLIAIFAFGMP 60

Query: 62  IDMAFAAAGYGFIYGLWPIAWIIVAAVFLYKLTVASGQFDIIRSSVISITDDQRLQVLLI 121
            +MA +AA  G   GL PI WI++  ++L++LT  +G F +++ S+  ITDD+RLQ+LLI
Sbjct: 61  ANMAGSAALLGAATGLVPIGWIVLNIIYLHRLTTENGSFKVLQDSLARITDDRRLQLLLI 120

Query: 122 GFSFGALLEGAAGFGAPVAITGALLVGLGFKPLYAAGLCLIANTAPVAFGALGVPILVAG 181
            F FGA  EGAAGFG PVA+TGA+L+GLGF PL A+GL LIANTAPVAFGALG PI+   
Sbjct: 121 AFCFGAFFEGAAGFGTPVAVTGAILIGLGFSPLAASGLALIANTAPVAFGALGTPIITLA 180

Query: 182 QVTGIDPFHIGAMAGRQLPFLSVLVPFWLVAMMDGWKGVKETWPAALVAGGSFAVTQFFT 241
           +VTG+D   +  M GRQLPF SVLVPFWL+    GW+ + E WPA LVAG SFAV QFF 
Sbjct: 181 KVTGLDEMQLSMMVGRQLPFFSVLVPFWLIWAFAGWRKMLEIWPAILVAGVSFAVPQFFV 240

Query: 242 SNYIGPELPDITSALVSIVSLALFLKVWRPKNTETAISM-GQSAGAMVVNKPSSGGPVPS 300
           SNY GP L D+ +AL+S+  L  FLKVW+P    T+ ++ G+   + V   P       +
Sbjct: 241 SNYHGPMLVDVIAALISMACLTGFLKVWKPARVHTSAALSGRVDDSKVEESPDEKTAASA 300

Query: 301 EYSLG---QIIRAWSPFLILTVLVTIWTMKPFKALF----------------------AP 335
            ++      ++RAW P++ILTV V  W  + FK +F                      + 
Sbjct: 301 TFASDARPTVMRAWMPWIILTVFVFAWGTQGFKNMFDIRPAMDPQTHSAKLDPQGKPVSE 360

Query: 336 GGAFYSLVINFQIPHLHQQVLKAAPIVAQPTPMDAVFKFDPLSAGGTAIFIAAIISIFIL 395
               ++  + F    LH QV K  P+V QP P +A++KF  L++ G+ I +AAI    ++
Sbjct: 361 ANPIFAPALTFTT--LHLQVEKVPPVVPQPKPEEAIYKFTWLTSTGSGILLAAIFGGLLM 418

Query: 396 GVGIKKGIGVFAETLISLKWPILSIGMVLAFAFVTNYSGMSTTLALVLAGTGVMFPFFSP 455
           G  I + +  +  TL  +++ + +I  +LA  F+T YSG+  T+ L  A TG+ +P F  
Sbjct: 419 GYSIPQLVSQYLRTLWVVRYSLTTIAAMLALGFITRYSGLDATMGLAFAATGIFYPMFGT 478

Query: 456 FLGWLGVFLTGSDTSSNALFGSLQSTTAQQINVSDTLLVAANTSGGVTGKMISPQSIAVA 515
            LGWLGV LTGSDT+SN LFG LQ  T++Q+ +S  L+ AAN+SGGV GKM+  QSI VA
Sbjct: 479 LLGWLGVALTGSDTASNVLFGGLQRVTSEQLGISPILMAAANSSGGVMGKMVDAQSIVVA 538

Query: 516 CAATGMVGRESELFRYTVKHSLIFASVIGIITLLQAYV 553
             AT   G E E+ RY   HS++ A ++G +  LQAYV
Sbjct: 539 STATRWYGHEGEILRYVFFHSIVLAILVGGLVTLQAYV 576


Lambda     K      H
   0.327    0.141    0.424 

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: 988
Number of extensions: 40
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: 560
Length of database: 587
Length adjustment: 36
Effective length of query: 524
Effective length of database: 551
Effective search space:   288724
Effective search space used:   288724
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