GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuA in Haloterrigena daqingensis JX313

Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate WP_076581084.1 BB347_RS10035 glutamine synthetase

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



>NCBI__GCF_001971705.1:WP_076581084.1
          Length = 451

 Score =  182 bits (463), Expect = 1e-50
 Identities = 139/451 (30%), Positives = 210/451 (46%), Gaps = 42/451 (9%)

Query: 6   DFLKKNRVTEIEAIIPDMAGIARGKIIPRSKFESGESMRLPQAVMIQTVTGDYPEDGTLT 65
           D +++N +  +     D+ G  +   +P  + E   +             G Y +  ++ 
Sbjct: 15  DDIEENDIDFLRLQFTDILGTVKNVSVPARQAEKAFA------------EGIYFDGSSIE 62

Query: 66  G---VTDPDMVCVPDASTIRMIPWAV---DPTAQVIHDCVHF-DGTPVAISPRRVLRRVL 118
           G   + + DM  VPD +T  ++PW       +A++I D  +   G P    PRRVLR  L
Sbjct: 63  GFVRIQESDMRLVPDPNTFAILPWRNREDGASARMICDVYNTTSGEPFEGDPRRVLRNAL 122

Query: 119 ELYKAKGWKPVIAPELEFYLVDMNKDPDLPLQPPIGRTGRPETGRQAYSIEAVNEF-DPL 177
           +     G++   APE EF+L + +++         GR          Y   A  +    +
Sbjct: 123 DRAHEMGYEVNAAPEPEFFLFEEDEE---------GRATTTTNDAGGYFDLAPKDLASDV 173

Query: 178 FEDIYEYCEVQELEVDTLIHEVGAAQMEINFMHGDPLKLADSVFLFKRTVREAALRHKMY 237
             DI    E    EV+   HEV   Q EINF + D L  AD+V  F+  VR  A +H  +
Sbjct: 174 RRDIIYGLENMGFEVEASHHEVAEGQHEINFEYDDALTTADNVATFRTVVRAIAAQHDYH 233

Query: 238 ATFMAKPMEGEPGSAMHMHQSLVDEETGHNLFTGPDGK--PTSLFTSYIAGLQKYTPALM 295
           ATFM KP+    GS MH H SL  E+ G N F   D +   +    ++ AG+ ++ PA+ 
Sbjct: 234 ATFMPKPIPEINGSGMHTHISLFTED-GENAFHDEDDEFNLSEEARAFTAGVLEHAPAIT 292

Query: 296 PIFAPYINSYRRLSRFMAAPINVAWGYDNRTVGFRIPHSG-PAARRIENRIPGVDCNPYL 354
            +  P +NSY+RL     AP+ VAW   NR+   R P +  PAA R+E R P   CNPYL
Sbjct: 293 AVANPTVNSYKRLVPGYEAPVYVAWSDRNRSSLIRKPAARVPAASRVELRSPDPSCNPYL 352

Query: 355 AIAATLAAGYLGMTQKLEATEPLLSDGYELPYQ---------LPRNLEEGLTLMGACEPI 405
           AIA  + AG  G+ Q LE  +P+  + YE   Q         LP NL E +  +   + +
Sbjct: 353 AIAVMIHAGLDGIEQDLECPDPVRENIYEFDEQKREEYGIDTLPANLGEAVDALEEDDAM 412

Query: 406 AEVLGEKFVKAYLALKETEYEAFFRVISSWE 436
            + LGE   + ++  K  E+E +   +S WE
Sbjct: 413 FDALGEHIGEKFVEAKRQEFEEYLIDVSEWE 443


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: 522
Number of extensions: 39
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: 451
Length adjustment: 33
Effective length of query: 411
Effective length of database: 418
Effective search space:   171798
Effective search space used:   171798
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