GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuA in Marinobacter adhaerens HP15

Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate GFF963 HP15_942 glutamate-putrescine ligase

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



>lcl|FitnessBrowser__Marino:GFF963 HP15_942 glutamate-putrescine
           ligase
          Length = 454

 Score =  622 bits (1605), Expect = 0.0
 Identities = 290/449 (64%), Positives = 374/449 (83%), Gaps = 1/449 (0%)

Query: 11  NEANAFLKEHPEVLYVDLLIADMNGVVRGKRIERTSLHKVYEKGINLPASLFALDINGST 70
           + A++FL+ HPE+ +VDLLI DMNG+VRGKR++ ++L KV+E+G+ +PAS+FAL+I G+T
Sbjct: 6   SSADSFLQAHPELQFVDLLIPDMNGIVRGKRVDPSALAKVFERGVAMPASIFALNIQGTT 65

Query: 71  VESTGLGLDIGDADRICYPIPNTLCNEPWQKRPTAQLLMTMHELEGE-PFFADPREVLAN 129
           VE TGLGLDIG+ADR+C PI NTL  EPWQKRPTAQLL+TM+EL+ E PFFADPR VL N
Sbjct: 66  VEETGLGLDIGEADRVCLPIENTLTMEPWQKRPTAQLLLTMYELDRETPFFADPRVVLQN 125

Query: 130 VVRKFDDMGLTICAAFELEFYLIDQENVNGRPQPPRSPVSGKRPHSTQVYLIDDLDEYVD 189
           ++++F+D+GLT  AAFELEFYLIDQEN+ GRPQPP+SP+SGKRP  TQ Y IDDLDEY +
Sbjct: 126 IIKRFEDLGLTPVAAFELEFYLIDQENLAGRPQPPKSPLSGKRPAGTQAYSIDDLDEYAE 185

Query: 190 CLQDILEGAKEQGIPADAIVKESAPAQFEVNLHHVADPIKACDYAVLLKRLIKNIAYDHE 249
            L D+L+ A EQ +PADA+V ESAP QFEVNLH+V D ++ACD+A LLKRLIKN+AYDHE
Sbjct: 186 FLADVLDAAHEQELPADALVAESAPGQFEVNLHYVDDAVQACDHATLLKRLIKNMAYDHE 245

Query: 250 MDTTFMAKPYPGQAGNGLHVHISILDKDGKNIFASEDPEQNAALRHAIGGVLETLPAQMA 309
           MDTTFMAKPY  QAG+G+H+H+S++D +G+N+FA +  + N  LR A+GG++ T+   MA
Sbjct: 246 MDTTFMAKPYHNQAGSGMHLHVSLVDGEGRNVFAGDAEQPNDMLRWAVGGLVATMNDAMA 305

Query: 310 FLCPNVNSYRRFGAQFYVPNSPCWGLDNRTVAIRVPTGSADAVRIEHRVAGADANPYLLM 369
             CPN+NSYRRF  ++YVP++  WG+DNRT ++R+P G  +A+RIEHRVAGADANPYLLM
Sbjct: 306 LFCPNINSYRRFSPEYYVPSAATWGVDNRTASLRLPGGDPEALRIEHRVAGADANPYLLM 365

Query: 370 ASVLAGVHHGLTNKIEPGAPVEGNSYEQNEQSLPNNLRDALRELDDSEVMAKYIDPKYID 429
           A+VLAG+H+G++N+IEP     GN++EQ+E SL NNLRDALREL  S+VMA Y+  +++D
Sbjct: 366 AAVLAGIHYGISNRIEPPPVTVGNAHEQHEASLVNNLRDALRELGQSKVMADYLGSQFLD 425

Query: 430 IFVACKESELEEFEHSISDLEYNWYLHTV 458
           +FVACKE EL EFE +ISDLEY WYLHTV
Sbjct: 426 VFVACKEHELNEFEMTISDLEYLWYLHTV 454


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: 745
Number of extensions: 30
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: 458
Length of database: 454
Length adjustment: 33
Effective length of query: 425
Effective length of database: 421
Effective search space:   178925
Effective search space used:   178925
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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