GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Pseudomonas putida KT2440

Align Histidine transport ATP-binding protein HisP (characterized)
to candidate PP_3597 PP_3597 Amino-acid ABC transporter, ATP-binding protein

Query= SwissProt::P02915
         (258 letters)



>FitnessBrowser__Putida:PP_3597
          Length = 260

 Score =  234 bits (596), Expect = 2e-66
 Identities = 125/247 (50%), Positives = 166/247 (67%), Gaps = 12/247 (4%)

Query: 7   LHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEGAIIVN 66
           + +  L+K YG   VL+ + LQ R G+ I + G SGSGKST +RCIN LE   +G+I V+
Sbjct: 21  IRIEGLNKHYGAFHVLRDIDLQVREGERIVLCGPSGSGKSTLIRCINRLEVAQQGSIQVD 80

Query: 67  GQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLSK 126
           G ++            A   +   +R+ + MVFQHFNL+ HM+VL+N + AP  V GLS+
Sbjct: 81  GIDL-----------AATTREAAQVRSDIGMVFQHFNLFPHMSVLDNCLLAPTSVRGLSR 129

Query: 127 HDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPTSALDP 186
            DA ERA  YL+KVGI+ +A  KYP  LSGGQQQRV+IARAL M+P ++LFDEPTSALDP
Sbjct: 130 KDAEERARMYLSKVGIESQAH-KYPSQLSGGQQQRVAIARALCMKPRIMLFDEPTSALDP 188

Query: 187 ELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVFGNPQS 246
           E+V EVL ++ QLA  G TM+ VTHEMGFAR V+  V+FL  G+I E+  P+  F  P++
Sbjct: 189 EMVAEVLDVLVQLAGTGMTMLCVTHEMGFARQVAERVLFLEGGQIIEDSPPQVFFNQPRT 248

Query: 247 PRLQQFL 253
            R + FL
Sbjct: 249 ERAKAFL 255


Lambda     K      H
   0.319    0.136    0.383 

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: 193
Number of extensions: 8
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: 258
Length of database: 260
Length adjustment: 24
Effective length of query: 234
Effective length of database: 236
Effective search space:    55224
Effective search space used:    55224
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 (21.7 bits)
S2: 47 (22.7 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