GapMind for catabolism of small carbon sources

 

Aligments for a candidate for hisP in Pseudomonas fluorescens FW300-N1B4

Align histidine transport ATP-binding protein hisP (characterized)
to candidate Pf1N1B4_3175 Histidine ABC transporter, ATP-binding protein HisP (TC 3.A.1.3.1)

Query= CharProtDB::CH_003210
         (257 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3175 Histidine ABC
           transporter, ATP-binding protein HisP (TC 3.A.1.3.1)
          Length = 254

 Score =  353 bits (906), Expect = e-102
 Identities = 172/253 (67%), Positives = 216/253 (85%), Gaps = 1/253 (0%)

Query: 5   KLNVIDLHKRYGEHEVLKGVSLQANAGDVISIIGSSGSGKSTFLRCINFLEKPSEGSIVV 64
           KL +  LHK YG+H+VLKGVSL+A  GDVIS+IG+SGSGKSTFLRCINFLE+P++G++ +
Sbjct: 3   KLTIEGLHKSYGDHQVLKGVSLKAKTGDVISLIGASGSGKSTFLRCINFLEQPNDGAMSL 62

Query: 65  NGQTINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLS 124
           +GQTI ++ D+ G ++VAD ++L+ +RTRL MVFQHFNLWSHMTVLEN+  AP +VLG S
Sbjct: 63  DGQTIRMIHDRHG-MRVADADELQRIRTRLAMVFQHFNLWSHMTVLENITMAPRRVLGCS 121

Query: 125 KQEARERAVKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPEVLLFDEPTSALD 184
           KQEA +RA +YL KVG+  R   +YP  LSGGQQQRV+IARALAMEPEV+LFDEPTSALD
Sbjct: 122 KQEAEDRARRYLDKVGLAARVADQYPAFLSGGQQQRVAIARALAMEPEVMLFDEPTSALD 181

Query: 185 PELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSTHVIFLHQGKIEEEGAPEQLFGNPQ 244
           PELVGEVL+++Q LAEEG+TM++VTHEM FAR VS+ V+FLHQG +EEEGAPE + GNP+
Sbjct: 182 PELVGEVLKVIQGLAEEGRTMIMVTHEMSFARKVSSQVLFLHQGLVEEEGAPEDVLGNPK 241

Query: 245 SPRLQRFLKGSLK 257
           S RL++FL G+LK
Sbjct: 242 SERLKQFLSGNLK 254


Lambda     K      H
   0.318    0.134    0.375 

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: 222
Number of extensions: 2
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: 257
Length of database: 254
Length adjustment: 24
Effective length of query: 233
Effective length of database: 230
Effective search space:    53590
Effective search space used:    53590
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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