GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutV in Bacteroides thetaiotaomicron VPI-5482

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate 350819 BT1291 spermidine/putrescine transport ATP-binding protein (NCBI ptt file)

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



>FitnessBrowser__Btheta:350819
          Length = 463

 Score =  157 bits (397), Expect = 4e-43
 Identities = 86/263 (32%), Positives = 147/263 (55%), Gaps = 30/263 (11%)

Query: 7   SKIEVKNVFKIFGNRSKEALELIRQNKTKDQVLAETGCVVGVNDLSLSIGTGEIFVIMGL 66
           S IEV +V K FG+++                         ++D++L++  GE   I+G 
Sbjct: 8   SIIEVSHVSKFFGDKT------------------------ALDDVTLNVKKGEFVTILGP 43

Query: 67  SGSGKSTLVRHFNRLIDPTSGAILVDGEDILQLDMDALREFRRHKISMVFQSFGLLPHKS 126
           SG GK+TL+R        + G I + G++I Q          +  ++ VFQ + L PH +
Sbjct: 44  SGCGKTTLLRLIAGFQTASEGEIRISGKEITQTPP------HKRPVNTVFQKYALFPHLN 97

Query: 127 VLDNVAYGLKVRGESKQVCAERALHWINTVGLKGYENKYPHQLSGGMRQRVGLARALAAD 186
           V DN+A+GLK++   KQ   ++    +  VG+  YE +    LSGG +QRV +ARA+  +
Sbjct: 98  VYDNIAFGLKLKKTPKQTIGKKVKAALKMVGMTDYEYRDVDSLSGGQQQRVAIARAIVNE 157

Query: 187 TDIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTIVFITHDLDEAVRIGNRIAILKDGK 246
            +++L+DE  +ALD  +R +MQ +L E+ K+L  T V++THD +EA+ + + I ++ +GK
Sbjct: 158 PEVLLLDEPLAALDLKMRKDMQMELKEMHKSLGITFVYVTHDQEEALTLSDTIVVMSEGK 217

Query: 247 LIQVGTPREILHSPADEYVDRFV 269
           + Q+GTP +I + P + +V  F+
Sbjct: 218 IQQIGTPIDIYNEPINSFVADFI 240


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: 302
Number of extensions: 19
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: 463
Length adjustment: 29
Effective length of query: 247
Effective length of database: 434
Effective search space:   107198
Effective search space used:   107198
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