GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PS417_17605 in Pseudomonas fluorescens FW300-N1B4

Align ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale)
to candidate Pf1N1B4_4794 Histidine ABC transporter, ATP-binding protein HisP (TC 3.A.1.3.1)

Query= uniprot:A0A1N7U8S3
         (276 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4794 Histidine ABC
           transporter, ATP-binding protein HisP (TC 3.A.1.3.1)
          Length = 253

 Score =  389 bits (1000), Expect = e-113
 Identities = 201/251 (80%), Positives = 217/251 (86%)

Query: 26  KLQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAGVITL 85
           KL VE ++KR+G++EVLKGVSLNAR GDV+S+IGASGSGKSTMLRCINFLE+ D G I L
Sbjct: 3   KLTVENLYKRFGDNEVLKGVSLNARAGDVVSMIGASGSGKSTMLRCINFLERADEGAIVL 62

Query: 86  DGISIEMRQGRAGTRAPHQDQLQNLRTRLAMVFQHFNLWSHMTVLENITMAPRRVLDVSA 145
           DG  +  R G  G R  +  QLQ LRTRLAMVFQHFNLWSH+TVLENI +AP RVL VS 
Sbjct: 63  DGERVITRPGAGGMRVANPAQLQRLRTRLAMVFQHFNLWSHLTVLENIILAPCRVLGVSR 122

Query: 146 AEAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEPTSALDP 205
             AE+ AR YLDKVGLP RVADQYPAFLSGGQQQRVAIARALA+EPEI+LFDEPTSALDP
Sbjct: 123 KAAEESARAYLDKVGLPQRVADQYPAFLSGGQQQRVAIARALAVEPEILLFDEPTSALDP 182

Query: 206 ELVGEVLKVIQTLAEEGRTMLMVTHEMGFARQVSSQVLFLHQGRVEEHGDARILDQPNSE 265
           ELVGEVLKVIQ LAEEGRTMLMVTHEMGFARQVSSQVLFLHQGRVEE GDA ILD+P SE
Sbjct: 183 ELVGEVLKVIQALAEEGRTMLMVTHEMGFARQVSSQVLFLHQGRVEEQGDATILDRPESE 242

Query: 266 RLQQFLSNRLK 276
           RLQQFLS RLK
Sbjct: 243 RLQQFLSGRLK 253


Lambda     K      H
   0.319    0.133    0.372 

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: 295
Number of extensions: 3
Number of successful extensions: 1
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: 253
Length adjustment: 25
Effective length of query: 251
Effective length of database: 228
Effective search space:    57228
Effective search space used:    57228
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 (21.8 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, the preprint on GapMind for carbon sources, 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