GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livJ in Pseudomonas fluorescens GW456-L13

Align Leucine ABC transporter subunit substrate-binding protein LivK (characterized, see rationale)
to candidate PfGW456L13_4606 High-affinity leucine-specific transport system, periplasmic binding protein LivK (TC 3.A.1.4.1)

Query= uniprot:A0A160A0J6
         (375 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4606
          Length = 375

 Score =  709 bits (1831), Expect = 0.0
 Identities = 355/375 (94%), Positives = 367/375 (97%)

Query: 1   MTKATKQISKLFAAMVLAGVASHSFAADTIKIGIAGPKTGPVAQYGDMQFSGSKMAIEQI 60
           MTKATKQISKLFAAMVLAGVASHSFAADTIKIGIAGPKTGPVAQYGDMQFSG+KMAIEQI
Sbjct: 1   MTKATKQISKLFAAMVLAGVASHSFAADTIKIGIAGPKTGPVAQYGDMQFSGAKMAIEQI 60

Query: 61  NAKGGVNGKQLVAVEYDDACDPKQAVAVANKVVNDGIKFVVGHLCSSSTQPASDIYEDEG 120
           NAKGGV+GK+L AVEYDDACDPKQAVAVANKVVNDG+KFVVGHLCSSSTQPASDIYEDEG
Sbjct: 61  NAKGGVDGKKLEAVEYDDACDPKQAVAVANKVVNDGVKFVVGHLCSSSTQPASDIYEDEG 120

Query: 121 VVMITPAATSPDITARGYKMIFRTIGLDSAQGPAAGNYIADHVKPKIVAVLHDKQQYGEG 180
           V+MITPAATSPDITARGYKM+FRTIGLDSAQGPAAGNYIAD VKPKIVAVLHDKQQYGEG
Sbjct: 121 VIMITPAATSPDITARGYKMVFRTIGLDSAQGPAAGNYIADFVKPKIVAVLHDKQQYGEG 180

Query: 181 IASAVKKTLEDKGVKVAVFEGVNAGDKDFSSMIAKLKQANVDFVYYGGYHPELGLILRQS 240
           IASAVKKTLE KGVKVAVFEGVNAGDKDFSSMIAKLKQANVDFVYYGGYHPELGLILRQS
Sbjct: 181 IASAVKKTLEGKGVKVAVFEGVNAGDKDFSSMIAKLKQANVDFVYYGGYHPELGLILRQS 240

Query: 241 QEKGLKAKFMGPEGVGNDSISQIAKESSEGLLVTLPKSFDQDPANIALADAFKAKKEDPS 300
            EKGLKAKFMGPEGVGNDSISQIAK++SEGLLVTLPKSFDQDPAN+ALADAFKAKKEDPS
Sbjct: 241 AEKGLKAKFMGPEGVGNDSISQIAKDASEGLLVTLPKSFDQDPANVALADAFKAKKEDPS 300

Query: 301 GPFVFPSYSAVTVIADAIKAAKSEDAGKVAEAIHAGTFKTPTGDLSFDKNGDLKDFKFVV 360
           GPFVFP+YSAVTVIAD IKAAKSED+ KVAEAIHAGTFKTPTGDLSFD+ GDLKDFKFVV
Sbjct: 301 GPFVFPAYSAVTVIADGIKAAKSEDSAKVAEAIHAGTFKTPTGDLSFDEKGDLKDFKFVV 360

Query: 361 YEWHFGKPKTEASPQ 375
           YEWHFGKPKTEA PQ
Sbjct: 361 YEWHFGKPKTEAKPQ 375


Lambda     K      H
   0.314    0.132    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: 709
Number of extensions: 30
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: 375
Length of database: 375
Length adjustment: 30
Effective length of query: 345
Effective length of database: 345
Effective search space:   119025
Effective search space used:   119025
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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