GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Shew_2731 in Knoellia flava TL1

Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate WP_035949051.1 N798_RS12935 cation acetate symporter

Query= reanno::PV4:5209923
         (572 letters)



>NCBI__GCF_000768675.1:WP_035949051.1
          Length = 551

 Score =  179 bits (454), Expect = 3e-49
 Identities = 154/513 (30%), Positives = 237/513 (46%), Gaps = 74/513 (14%)

Query: 9   LIVGFTFA-LYIGIAIWSRAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFISLAGIVS 67
           +  GF    L + + + S   S  EFY A GG     NG+A A D++SAASF+ +AG ++
Sbjct: 25  IFAGFVLVTLVVIVKLASGKKSAGEFYTASGGFSGRQNGIAIAGDYLSAASFLGIAGAIA 84

Query: 68  FVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQAARTVAVVCAIFI 127
             GYDG +Y +G+   +++  L +A  +R  G+ T+ D +  R   +  R       + +
Sbjct: 85  LQGYDGFLYSIGFLVAWLVALLLVAELMRNTGRLTMADVLSYRLKQRPVRIATATSVLAV 144

Query: 128 CFTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVV----FFYAVLGGMKGITYTQVAQYC 183
            F Y+  QM G G + S  L VE +    I +AVV      Y ++GGM+G T+ Q+ +  
Sbjct: 145 SFFYLLAQMAGAGGLVSLLLGVEGEGAQNIVIAVVGIVMIAYVLIGGMRGTTWVQIIKAV 204

Query: 184 VLIFAFMVPAIFISVMMTGHILPQLGFG-AELVDAAGNNTGVYLLEKLDGLSAQLGFSQY 242
           +LI A        + +MT  +L + GF  + L DAA  N    + EKL     + G S  
Sbjct: 205 LLIAA--------TAIMTVWVLGKYGFNLSGLFDAAIQN-NPKVGEKLLEPGVKYGVSTT 255

Query: 243 TEGSKGMIDVFFITGALMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMY--TTI 300
           T+     ID   ++ AL+ GTAGLPHV+ RF+TVP  K AR S  WA+  I   Y  T +
Sbjct: 256 TK-----IDFISLSLALVLGTAGLPHVLQRFYTVPTSKQARKSVEWAIWLIGGFYLLTLV 310

Query: 301 PALAAFSRVNMIETINGPESTGVAYETAPDWIKNWEKTGLIKWDDKNNDGKIYYAKGETN 360
               A + V   E    P   G A   AP                               
Sbjct: 311 VGYGAGALVGAEEINKAP---GKANAAAP------------------------------- 336

Query: 361 EMKIDRDIMVLATPEIANLPAWVIALVAAGGLAAALSTSAGLLLVISTSVSHDLLKKNF- 419
                     L   E+   P   + +V+    A  L+  AGL +  S + +HD+ K+   
Sbjct: 337 ----------LLAFELGGSP--FLGIVSGIAFATILAVVAGLTITASATFAHDIYKEVIK 384

Query: 420 MPDISDKQELLYARIAA-ALGI--VMAGYFGINPPGFVAAVVAIAFGLAASSLFPAIIMG 476
             D +   E+  ARI+A A+GI  ++ G F  +    +A +VA+AF +AAS+  P I+  
Sbjct: 385 RGDTTSDNEVRVARISAVAIGIIAILGGMFAKSQN--IAFLVALAFAVAASANLPTILYS 442

Query: 477 IFSRTMNKEGAIAGMVIGLLFSASYIIYFKFVN 509
           +F +  N  GA+  +  GL+ +   II+   V+
Sbjct: 443 LFWKRFNTRGALWSIYGGLISTIGLIIFSPVVS 475


Lambda     K      H
   0.326    0.140    0.423 

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: 797
Number of extensions: 45
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 572
Length of database: 551
Length adjustment: 36
Effective length of query: 536
Effective length of database: 515
Effective search space:   276040
Effective search space used:   276040
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 24 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