GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuA in Klebsiella michiganensis M5al

Align Glutamate--putrescine ligase (EC 6.3.1.11) (characterized)
to candidate BWI76_RS10710 BWI76_RS10710 gamma-glutamylputrescine synthetase

Query= reanno::Koxy:BWI76_RS10710
         (472 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS10710 BWI76_RS10710
           gamma-glutamylputrescine synthetase
          Length = 472

 Score =  964 bits (2491), Expect = 0.0
 Identities = 472/472 (100%), Positives = 472/472 (100%)

Query: 1   METNIVEVENFVQQSEERRVSAFTWEVKRYLERYPNTQYVDVLLTDLNGCFRGKRIPVSG 60
           METNIVEVENFVQQSEERRVSAFTWEVKRYLERYPNTQYVDVLLTDLNGCFRGKRIPVSG
Sbjct: 1   METNIVEVENFVQQSEERRVSAFTWEVKRYLERYPNTQYVDVLLTDLNGCFRGKRIPVSG 60

Query: 61  LSKLEKGCYFPASVFAMDILGNVVEEAGLGQEMGEPDRTCVPVLGTLTPSAADPEYIGQV 120
           LSKLEKGCYFPASVFAMDILGNVVEEAGLGQEMGEPDRTCVPVLGTLTPSAADPEYIGQV
Sbjct: 61  LSKLEKGCYFPASVFAMDILGNVVEEAGLGQEMGEPDRTCVPVLGTLTPSAADPEYIGQV 120

Query: 121 LLTMVDEDGAPFDVEPRNVLNRLWQQLRQRGLFPVVAVELEFYLLDRKRDAEGYLQPPCA 180
           LLTMVDEDGAPFDVEPRNVLNRLWQQLRQRGLFPVVAVELEFYLLDRKRDAEGYLQPPCA
Sbjct: 121 LLTMVDEDGAPFDVEPRNVLNRLWQQLRQRGLFPVVAVELEFYLLDRKRDAEGYLQPPCA 180

Query: 181 PGTGDRNTQSQVYSVDNLNHFADVLNEIDEIAQLQLIPADGAVAEASPGQFEINLHHTDN 240
           PGTGDRNTQSQVYSVDNLNHFADVLNEIDEIAQLQLIPADGAVAEASPGQFEINLHHTDN
Sbjct: 181 PGTGDRNTQSQVYSVDNLNHFADVLNEIDEIAQLQLIPADGAVAEASPGQFEINLHHTDN 240

Query: 241 VLDACDDALALKRLVRLMAEKHKMHATFMAKPYEEHAGSGMHIHISMQNNKGENVLADAD 300
           VLDACDDALALKRLVRLMAEKHKMHATFMAKPYEEHAGSGMHIHISMQNNKGENVLADAD
Sbjct: 241 VLDACDDALALKRLVRLMAEKHKMHATFMAKPYEEHAGSGMHIHISMQNNKGENVLADAD 300

Query: 301 GEDSAMLKRALAGMIDLMPASMALLAPNVNSYRRFQPGMYVPTQASWGHNNRTVALRIPC 360
           GEDSAMLKRALAGMIDLMPASMALLAPNVNSYRRFQPGMYVPTQASWGHNNRTVALRIPC
Sbjct: 301 GEDSAMLKRALAGMIDLMPASMALLAPNVNSYRRFQPGMYVPTQASWGHNNRTVALRIPC 360

Query: 361 GDRHNHRVEYRVAGADANPYLVMAAIFAGILHGLDNPLPLQEEVEGNGLEQEGLPFPIRQ 420
           GDRHNHRVEYRVAGADANPYLVMAAIFAGILHGLDNPLPLQEEVEGNGLEQEGLPFPIRQ
Sbjct: 361 GDRHNHRVEYRVAGADANPYLVMAAIFAGILHGLDNPLPLQEEVEGNGLEQEGLPFPIRQ 420

Query: 421 SDALWEFMQNDHLRERLGERFCHVYHACKNDELLQFERLITETEIEWMLKNA 472
           SDALWEFMQNDHLRERLGERFCHVYHACKNDELLQFERLITETEIEWMLKNA
Sbjct: 421 SDALWEFMQNDHLRERLGERFCHVYHACKNDELLQFERLITETEIEWMLKNA 472


Lambda     K      H
   0.319    0.136    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: 956
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: 472
Length of database: 472
Length adjustment: 33
Effective length of query: 439
Effective length of database: 439
Effective search space:   192721
Effective search space used:   192721
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: 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 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