GapMind for catabolism of small carbon sources

 

Alignments 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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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