Aligments for a candidate for puuA in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Aligments for a candidate for puuA in Dinoroseobacter shibae DFL-12

Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate 3608834 Dshi_2226 Glutamate--putrescine ligase (RefSeq)

Query= reanno::BFirm:BPHYT_RS23160
         (444 letters)



>FitnessBrowser__Dino:3608834
          Length = 456

 Score =  466 bits (1200), Expect = e-136
 Identities = 225/438 (51%), Positives = 293/438 (66%), Gaps = 1/438 (0%)

Query: 7   FLKKNRVTEIEAIIPDMAGIARGKIIPRSKFESGESMRLPQAVMIQTVTGDYPEDGTLTG 66
           +L+  R+ E+E I+ D+AG+ARGK +P +KF    S  LP ++  QT+TG + E   L G
Sbjct: 20  YLEGRRLDEVECIVADLAGVARGKAMPAAKFARQMSFYLPNSIFFQTITGGWAE-AALDG 78

Query: 67  VTDPDMVCVPDASTIRMIPWAVDPTAQVIHDCVHFDGTPVAISPRRVLRRVLELYKAKGW 126
            T+PDMV  PD ST    PW  D T Q+IHD     G P+ ++PR VL+RV+ LYKA+GW
Sbjct: 79  FTEPDMVLKPDFSTATPAPWTADWTLQIIHDIEDQSGAPMPVAPRNVLKRVIALYKARGW 138

Query: 127 KPVIAPELEFYLVDMNKDPDLPLQPPIGRTGRPETGRQAYSIEAVNEFDPLFEDIYEYCE 186
           KPV+APE+EFYL   N DP + +QPP+GRTGR    RQAYS+ AV+E+ P+ +DIY++ E
Sbjct: 139 KPVVAPEMEFYLTARNIDPAIAIQPPMGRTGRRAAARQAYSMSAVDEYGPVIDDIYDFAE 198

Query: 187 VQELEVDTLIHEVGAAQMEINFMHGDPLKLADSVFLFKRTVREAALRHKMYATFMAKPME 246
            Q LE+D +  E GA Q+EIN  HGDPLKLAD VF FKR +REAALRH  +ATFMAKP++
Sbjct: 199 AQGLEIDGITQEGGAGQIEINLRHGDPLKLADEVFYFKRLIREAALRHDCFATFMAKPIQ 258

Query: 247 GEPGSAMHMHQSLVDEETGHNLFTGPDGKPTSLFTSYIAGLQKYTPALMPIFAPYINSYR 306
            EPGSAMH+H S+ D  TG N+FT PDG  T  F  +IAGLQ +   ++P++APY+NSYR
Sbjct: 259 DEPGSAMHIHHSVTDIATGENIFTAPDGTETPAFQHFIAGLQSHLGDVVPLYAPYVNSYR 318

Query: 307 RLSRFMAAPINVAWGYDNRTVGFRIPHSGPAARRIENRIPGVDCNPYLAIAATLAAGYLG 366
           R     AAPIN+ W  DNRT G R+P + PAARR+ENR+ G+DCNPYL IAA+LA GYLG
Sbjct: 319 RYVPENAAPINLEWARDNRTAGLRVPVANPAARRVENRLAGMDCNPYLGIAASLACGYLG 378

Query: 367 MTQKLEATEPLLSDGYELPYQLPRNLEEGLTLMGACEPIAEVLGEKFVKAYLALKETEYE 426
           +  +       + D Y     L   L   L L      + ++LG +F + Y  +K  EY 
Sbjct: 379 LLAEKPPKPQYVGDAYSGSEDLAPELGAALDLFSEATAVHDILGPEFCRVYEIVKRHEYT 438

Query: 427 AFFRVISSWERRHLLLHV 444
            F +VIS WER HLLL+V
Sbjct: 439 EFLQVISPWEREHLLLNV 456


Lambda     K      H
   0.321    0.138    0.418 

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: 671
Number of extensions: 26
Number of successful extensions: 2
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: 444
Length of database: 456
Length adjustment: 33
Effective length of query: 411
Effective length of database: 423
Effective search space:   173853
Effective search space used:   173853
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources