GapMind for catabolism of small carbon sources

 

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

Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate Pf1N1B4_2254 Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11)

Query= reanno::pseudo1_N1B4:Pf1N1B4_2254
         (426 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2254
           Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11)
          Length = 426

 Score =  871 bits (2251), Expect = 0.0
 Identities = 426/426 (100%), Positives = 426/426 (100%)

Query: 1   MNGVVRGKRIERTSLHKVYEKGINLPASLFALDINGSTVESTGLGLDIGDADRICYPIPD 60
           MNGVVRGKRIERTSLHKVYEKGINLPASLFALDINGSTVESTGLGLDIGDADRICYPIPD
Sbjct: 1   MNGVVRGKRIERTSLHKVYEKGINLPASLFALDINGSTVESTGLGLDIGDADRICYPIPD 60

Query: 61  TLCNEPWQKRPTAQLLMTMHELEGDPFFADPREVLRQVVAKFDEMGLTICAAFELEFYLI 120
           TLCNEPWQKRPTAQLLMTMHELEGDPFFADPREVLRQVVAKFDEMGLTICAAFELEFYLI
Sbjct: 61  TLCNEPWQKRPTAQLLMTMHELEGDPFFADPREVLRQVVAKFDEMGLTICAAFELEFYLI 120

Query: 121 DQENVNGRPQPPRSPISGKRPHSTQVYLIDDLDEYVDCLQDILEGAKEQGIPADAIVKES 180
           DQENVNGRPQPPRSPISGKRPHSTQVYLIDDLDEYVDCLQDILEGAKEQGIPADAIVKES
Sbjct: 121 DQENVNGRPQPPRSPISGKRPHSTQVYLIDDLDEYVDCLQDILEGAKEQGIPADAIVKES 180

Query: 181 APAQFEVNLHHVADPIKACDYAVLLKRLIKNIAYDHEMDTTFMAKPYPGQAGNGLHVHIS 240
           APAQFEVNLHHVADPIKACDYAVLLKRLIKNIAYDHEMDTTFMAKPYPGQAGNGLHVHIS
Sbjct: 181 APAQFEVNLHHVADPIKACDYAVLLKRLIKNIAYDHEMDTTFMAKPYPGQAGNGLHVHIS 240

Query: 241 ILDKDGKNIFASEDPEQNAALRHAIGGVLETLPAQMAFLCPNVNSYRRFGAQFYVPNSPC 300
           ILDKDGKNIFASEDPEQNAALRHAIGGVLETLPAQMAFLCPNVNSYRRFGAQFYVPNSPC
Sbjct: 241 ILDKDGKNIFASEDPEQNAALRHAIGGVLETLPAQMAFLCPNVNSYRRFGAQFYVPNSPC 300

Query: 301 WGLDNRTVAIRVPTGSSDAVRIEHRVAGADANPYLLMASVLAGVHHGLTNKIEPGAPVEG 360
           WGLDNRTVAIRVPTGSSDAVRIEHRVAGADANPYLLMASVLAGVHHGLTNKIEPGAPVEG
Sbjct: 301 WGLDNRTVAIRVPTGSSDAVRIEHRVAGADANPYLLMASVLAGVHHGLTNKIEPGAPVEG 360

Query: 361 NSYEQNEQSLPNNLRDALRELDDSEVMAKYIDPKYIDIFVACKESELEEFEHSISDLEYN 420
           NSYEQNEQSLPNNLRDALRELDDSEVMAKYIDPKYIDIFVACKESELEEFEHSISDLEYN
Sbjct: 361 NSYEQNEQSLPNNLRDALRELDDSEVMAKYIDPKYIDIFVACKESELEEFEHSISDLEYN 420

Query: 421 WYLHTV 426
           WYLHTV
Sbjct: 421 WYLHTV 426


Lambda     K      H
   0.318    0.137    0.411 

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: 904
Number of extensions: 17
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: 426
Length of database: 426
Length adjustment: 32
Effective length of query: 394
Effective length of database: 394
Effective search space:   155236
Effective search space used:   155236
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: 51 (24.3 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 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