GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lctP in Pseudomonas fluorescens FW300-N2C3

Align Glycolate permease, GlcA or YghK (substrates: L-lactate, D-lactate and glycolate) (characterized)
to candidate AO356_22315 AO356_22315 lactate permease

Query= TCDB::Q46839
         (560 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22315 AO356_22315 lactate
           permease
          Length = 587

 Score =  503 bits (1295), Expect = e-147
 Identities = 264/587 (44%), Positives = 364/587 (62%), Gaps = 32/587 (5%)

Query: 2   VTWTQMYMPMGGLGLSALVALIPIIFFFVALAVLRLKGHVAGAITLILSILIAIFAFKMP 61
           + W Q+Y P G   LS L+A +P++    +LA   +K H+A  + L  ++LIAIFAF MP
Sbjct: 1   MVWQQVYDPFGNAVLSTLLAAVPVVVMLASLAFFHVKAHLAALLALASALLIAIFAFGMP 60

Query: 62  IDMAFAAAGYGFIYGLWPIAWIIVAAVFLYKLTVASGQFDIIRSSVISITDDQRLQVLLI 121
           + MA +AA YG   GL PI WI++  +FL++LT  +G F +++ S+  ITDD+RLQ+LLI
Sbjct: 61  VGMAGSAALYGAANGLLPIGWIVLNIIFLHRLTTENGSFKVLQDSLARITDDRRLQLLLI 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 SFA+ QF  
Sbjct: 181 KVTGLDEMELSMMVGRQLPFFSVLVPFWLIWAFAGWRKMLEVWPAILVAGVSFAIPQFLV 240

Query: 242 SNYIGPELPDITSALVSIVSLALFLKVWRPKNTETAISM-----GQSAGAMVVNKPSSGG 296
           SNY GP L D+ +AL+S+  L  FLKVW+P    T+ ++          A    KP++  
Sbjct: 241 SNYHGPMLVDVIAALISMACLTGFLKVWKPATVHTSAALSGRVDNSKIDASEDEKPTASA 300

Query: 297 PVPSEYSLGQIIRAWSPFLILTVLVTIWTMKPFKALF----------------------A 334
              ++ +   + RAW P++ILTV V  W  + FK LF                       
Sbjct: 301 AFSND-ARPAVGRAWMPWIILTVFVFAWGTQGFKNLFDTRPALDPQTQSAKLDPQSKPMR 359

Query: 335 PGGAFYSLVINFQIPHLHQQVLKAAPIVAQPTPMDAVFKFDPLSAGGTAIFIAAIISIFI 394
                +S ++ F    +HQQ+ K  P+V QP   +AV+KF+  +A G+ IF+AAI+   +
Sbjct: 360 EANPIFSPLVTFGT--IHQQIEKVPPVVPQPKTEEAVYKFNWFTATGSGIFLAAILGGLL 417

Query: 395 LGVGIKKGIGVFAETLISLKWPILSIGMVLAFAFVTNYSGMSTTLALVLAGTGVMFPFFS 454
           +G  I + +  +  TL  +++ +++I  +LA  F+T YSG+  T+ L  A TG+ +P F 
Sbjct: 418 MGYSIPQLVHHYLRTLWVVRYSLITIVAMLALGFLTRYSGLDATMGLAFAATGIFYPMFG 477

Query: 455 PFLGWLGVFLTGSDTSSNALFGSLQSTTAQQINVSDTLLVAANTSGGVTGKMISPQSIAV 514
             LGWLGV LTGSDT+SN LFG LQ  T++Q+ +S  L+ AAN+SGGV GKM+  QSI V
Sbjct: 478 TLLGWLGVALTGSDTASNVLFGGLQRVTSEQLGISPVLMAAANSSGGVMGKMVDAQSIVV 537

Query: 515 ACAATGMVGRESELFRYTVKHSLIFASVIGIITLLQAYV--FTGMLV 559
           A  AT   G E E+ RY   HS++ A ++G +  LQAYV  FT M+V
Sbjct: 538 ASTATRWYGHEGEILRYVFFHSVVLAILVGGLVTLQAYVAPFTHMVV 584


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: 994
Number of extensions: 42
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: 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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