GapMind for catabolism of small carbon sources

 

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

Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate Pf1N1B4_4354 Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11)

Query= reanno::pseudo3_N2E3:AO353_08595
         (458 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4354
          Length = 458

 Score =  878 bits (2268), Expect = 0.0
 Identities = 430/458 (93%), Positives = 445/458 (97%)

Query: 1   MSVPPRAVQLNEANAFLKEHPEVLYVDLLIADMNGVVRGKRIERTSLHKVYEKGINLPAS 60
           MSVP RAVQLNEANAFLK++PEVLYVDLLIADMNGVVRGKRIERTSLHKVYEKGINLPAS
Sbjct: 1   MSVPLRAVQLNEANAFLKKYPEVLYVDLLIADMNGVVRGKRIERTSLHKVYEKGINLPAS 60

Query: 61  LFALDINGSTVESTGLGLDIGDADRICYPIPNTLCNEPWQKRPTAQLLMTMHELEGEPFF 120
           LFALDINGSTVESTGLGLDIGD+DRIC+PIPNTL  EPWQKRPTAQLLMTMHELEG+PFF
Sbjct: 61  LFALDINGSTVESTGLGLDIGDSDRICFPIPNTLSIEPWQKRPTAQLLMTMHELEGQPFF 120

Query: 121 ADPREVLANVVRKFDDMGLTICAAFELEFYLIDQENVNGRPQPPRSPVSGKRPHSTQVYL 180
           ADPREVL  VV KFDDMGLTICAAFELEFYLIDQ+NVNGRPQ PRSPVSGKRP STQVYL
Sbjct: 121 ADPREVLRQVVSKFDDMGLTICAAFELEFYLIDQDNVNGRPQSPRSPVSGKRPMSTQVYL 180

Query: 181 IDDLDEYVDCLQDILEGAKEQGIPADAIVKESAPAQFEVNLHHVADPIKACDYAVLLKRL 240
           IDDLDEYVDCLQDILEGAKEQGIPADAIVKESAPAQFEVNLHHV DPIKACDYAVLLKRL
Sbjct: 181 IDDLDEYVDCLQDILEGAKEQGIPADAIVKESAPAQFEVNLHHVNDPIKACDYAVLLKRL 240

Query: 241 IKNIAYDHEMDTTFMAKPYPGQAGNGLHVHISILDKDGKNIFASEDPEQNAALRHAIGGV 300
           +KNIAYDHEMDTTFMAKPYPGQAGNGLHVHISILDK+G NIFASEDPEQNAALRHAIGGV
Sbjct: 241 VKNIAYDHEMDTTFMAKPYPGQAGNGLHVHISILDKEGNNIFASEDPEQNAALRHAIGGV 300

Query: 301 LETLPAQMAFLCPNVNSYRRFGAQFYVPNSPCWGLDNRTVAIRVPTGSADAVRIEHRVAG 360
           LETLPAQMAFLCPNVNSYRRFGAQFYVPNSP WG+DNRTVA+RVPTGSADAVRIEHRVAG
Sbjct: 301 LETLPAQMAFLCPNVNSYRRFGAQFYVPNSPSWGIDNRTVAVRVPTGSADAVRIEHRVAG 360

Query: 361 ADANPYLLMASVLAGVHHGLTNKIEPGAPVEGNSYEQNEQSLPNNLRDALRELDDSEVMA 420
           ADANPYLLMASVLAG+HHGLTN+IEPGAPVEGNSYEQNEQSLPNNLRDALRELDDSEVMA
Sbjct: 361 ADANPYLLMASVLAGIHHGLTNEIEPGAPVEGNSYEQNEQSLPNNLRDALRELDDSEVMA 420

Query: 421 KYIDPKYIDIFVACKESELEEFEHSISDLEYNWYLHTV 458
           +YIDP YID+FVACKESEL EFE+SISDLEYNWYLHTV
Sbjct: 421 RYIDPLYIDVFVACKESELAEFENSISDLEYNWYLHTV 458


Lambda     K      H
   0.318    0.137    0.409 

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: 946
Number of extensions: 21
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: 458
Length of database: 458
Length adjustment: 33
Effective length of query: 425
Effective length of database: 425
Effective search space:   180625
Effective search space used:   180625
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.

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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