GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutV in Pseudomonas fluorescens FW300-N2C3

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate AO356_00615 AO356_00615 choline ABC transporter ATP-binding protein

Query= reanno::pseudo5_N2C3_1:AO356_09610
         (276 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_00615
          Length = 407

 Score =  258 bits (659), Expect = 1e-73
 Identities = 137/268 (51%), Positives = 188/268 (70%), Gaps = 4/268 (1%)

Query: 6   ISKIEVKNVFKIFGNRSKEALELIRQNKTKDQVLAETGCVVGVNDLSLSIGTGEIFVIMG 65
           +S I  ++V  IF  R K ALEL+ Q  ++ ++L +TG +VGV   +L I  GEI V+MG
Sbjct: 1   MSIIRFEDVDVIFAARPKPALELLDQGFSRPEILQKTGLIVGVEKANLEINKGEICVLMG 60

Query: 66  LSGSGKSTLVRHFNRLIDPTSGAILVDGE----DILQLDMDALREFRRHKISMVFQSFGL 121
           LSGSGKS+L+R  N L   + G + V+ E    DI       L+  R  +I+MVFQ F L
Sbjct: 61  LSGSGKSSLLRCINGLNTVSRGKLFVEHEGRQIDIASCTPAELKMMRTQRIAMVFQKFAL 120

Query: 122 LPHKSVLDNVAYGLKVRGESKQVCAERALHWINTVGLKGYENKYPHQLSGGMRQRVGLAR 181
           +P  +V +N+++GL+++G S++ C +     +  VGL  + NK P +LSGGM+QRVGLAR
Sbjct: 121 MPWLTVRENISFGLEMQGRSEKECRKLVDEKLELVGLTQWRNKKPDELSGGMQQRVGLAR 180

Query: 182 ALAADTDIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTIVFITHDLDEAVRIGNRIAI 241
           ALA D DI+LMDE FSALDPLIR  +QD+LL+LQ+ LHKTIVF++HDLDEA+++G RIAI
Sbjct: 181 ALAMDADILLMDEPFSALDPLIRQGLQDELLDLQRKLHKTIVFVSHDLDEALKLGTRIAI 240

Query: 242 LKDGKLIQVGTPREILHSPADEYVDRFV 269
           +KDGK+IQ  TP EI+ +PAD+YV  FV
Sbjct: 241 MKDGKIIQYSTPEEIVLNPADDYVRNFV 268


Lambda     K      H
   0.321    0.138    0.387 

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: 324
Number of extensions: 16
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: 276
Length of database: 407
Length adjustment: 28
Effective length of query: 248
Effective length of database: 379
Effective search space:    93992
Effective search space used:    93992
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 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