GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuA in Dyadobacter tibetensis Y620-1

Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate WP_025763368.1 X939_RS0111240 glutamine synthetase

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



>NCBI__GCF_000566685.1:WP_025763368.1
          Length = 453

 Score =  185 bits (469), Expect = 3e-51
 Identities = 129/379 (34%), Positives = 190/379 (50%), Gaps = 21/379 (5%)

Query: 71  DMVCVPDASTIRMIPWAVDPTAQVIHDCVHFDGTPVAI-SPRRVLRRVLELYKAKGWKPV 129
           D   VPD ST+R+  W +D TA V+ D V      + I +PR +L++ LE          
Sbjct: 79  DFHMVPDLSTLRIADW-LDKTAMVLCDLVDEKNHSLDIVAPRSILKKQLEAVAQDELACF 137

Query: 130 IAPELEFYLVDMNK----DPDLPLQPPIGRTGRPETGRQAYSIEAVNEFDPLFEDIYEYC 185
            A ELE+YL++ N     D +     P G         + Y I      +     +  + 
Sbjct: 138 AASELEYYLLENNYREAFDKNYQDLKPAGYY------LEDYHIMQGTRNEHFTSKVRRHL 191

Query: 186 EVQELEVDTLIHEVGAAQMEINFMHGDPLKLADSVFLFKRTVREAALRHKMYATFMAKPM 245
           +   + V+T   E G  Q E+N  + + L +AD+  ++K+ ++E A    +  TFMAK  
Sbjct: 192 KKSGVPVETSKGEWGLGQHELNVRYAEILPMADNHVVYKQCLKEVADAMGLSVTFMAKYS 251

Query: 246 EGEPGSAMHMHQSLVDEETGHNLFTGPDG----KPTSLFTSYIAGLQKYTPALMPIFAPY 301
             + GS+ H+H SL  +  G N F G       K + LF  ++ G  KY P +MP +AP 
Sbjct: 252 TDQAGSSSHIHMSLWKD--GKNAFIGDQVFGPVKGSDLFRWFLGGWIKYVPDVMPFYAPT 309

Query: 302 INSYRRLSRFMAAPINVAWGYDNRTVGFRIPHSGPAARRIENRIPGVDCNPYLAIAATLA 361
           +NSY+R      AP  +AW YDNRT GFR+  SG A+ RIE RIPG DCNPYLA AA+LA
Sbjct: 310 VNSYKRFVDGSWAPTRLAWSYDNRTAGFRVVGSG-ASLRIECRIPGADCNPYLAFAASLA 368

Query: 362 AGYLGMTQKLEATEPLLSDGYELPY--QLPRNLEEGLTLMGACEPIAEVLGEKFVKAYLA 419
           +G  G+  K+E       D Y   +  ++P  L E + L       +E  GE+ VK Y  
Sbjct: 369 SGLAGIKNKIEPPAIFEGDIYAAAHLPRVPYTLAEAIPLFENSTFASEAFGEEVVKHYTH 428

Query: 420 LKETEYEAFFRVISSWERR 438
             + E +A+   ++ WER+
Sbjct: 429 FFKQEQKAYNESVTDWERK 447


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: 489
Number of extensions: 19
Number of successful extensions: 6
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: 453
Length adjustment: 33
Effective length of query: 411
Effective length of database: 420
Effective search space:   172620
Effective search space used:   172620
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 24 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