GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuA in Phaeobacter inhibens BS107

Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate GFF1139 PGA1_c11540 gamma-glutamylputrescine synthetase PuuA

Query= reanno::pseudo13_GW456_L13:PfGW456L13_925
         (458 letters)



>FitnessBrowser__Phaeo:GFF1139
          Length = 448

 Score =  276 bits (707), Expect = 8e-79
 Identities = 156/434 (35%), Positives = 228/434 (52%), Gaps = 4/434 (0%)

Query: 26  VDLLIADMNGVVRGKRIERTSLHKVYEKGINLPASLFALDINGSTVESTGLGLDIGDADR 85
           + +   D+NG +RGKR+      K+ +    +P S   +D+ G  VE   L  + GDAD 
Sbjct: 18  IRIAACDLNGQMRGKRMPVGLADKLADGAARMPISTLNVDLWGRDVEDNPLVFETGDADG 77

Query: 86  ICYPIPDTLCNEPWQKRPTAQLLMTMHELEGEPFFADPREVLANVVRKFDEMGLTICAAF 145
           +  P        PW   P+A + M M+  +G PF  DPR VLA+V+ ++ + G  + AA 
Sbjct: 78  VMLPTERGAVPMPWLANPSALVPMAMYWEDGRPFMGDPRHVLADVLARYQQRGWRVVAAT 137

Query: 146 ELEFYLIDQENVNGRPQPPRSPVSGKRPHSTQVYLIDDLDEYVDCLQDILEGAKEQGIPA 205
           E+EF L+D      +P PP  P++G+      V  + +LD +     D+ EG+   GIPA
Sbjct: 138 EMEFSLLDDSGA--QPAPPIDPLTGRELDQQSVLSVAELDAFDAFFTDLYEGSDAMGIPA 195

Query: 206 DAIVKESAPAQFEVNLHHVADPIKACDYAVLLKRLIKNIAYDHEMDTTFMAKPYPGQAGN 265
            + + E+   QFE+NL+H  + ++A D A L K L+K +A  H    TFMAKPY  +AGN
Sbjct: 196 QSAISEAGLGQFEINLNH-QEAMRAADDAWLFKALVKGLARKHGFAATFMAKPYAEEAGN 254

Query: 266 GLHVHISILDKDGKNIFASEDPEQNAALRHAIGGVLETLPAQMAFLCPNVNSYRRFGAQF 325
           G+HVH S+ D+DG N+F       +  L +A+ G L  +PA    L P+ NSY R     
Sbjct: 255 GMHVHFSVEDEDGNNVFNDGTERGSGLLMNAVAGCLTAMPASTLILAPHGNSYDRLVPGA 314

Query: 326 YVPNSPCWGLDNRTVAIRVPTGSADAVRIEHRVAGADANPYLLMASVLAGVHHGLTNKIE 385
           + P S  W  +NRT AIR+P GS  A RIEHRVAG D NPYL++A VL     G+ +   
Sbjct: 315 HAPVSAAWAYENRTAAIRIPGGSPKARRIEHRVAGGDINPYLMLAVVLGAALAGIEDGAT 374

Query: 386 PGAPVEGNSYE-QNEQSLPNNLRDALRELDDSEVMAKYIDPKYIDIFVACKESELEEFEH 444
           P AP EGN YE      L  + + A+   D   ++A+ +  + I   V  K  E   F  
Sbjct: 375 PPAPSEGNIYEIDGLPQLAPDWKAAIDLFDSDPLIARILPDRVIRNLVMMKRQEQAGFAE 434

Query: 445 SISDLEYNWYLHTV 458
             ++  +  +L  V
Sbjct: 435 RPAESHWLSWLEAV 448


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: 569
Number of extensions: 27
Number of successful extensions: 3
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: 448
Length adjustment: 33
Effective length of query: 425
Effective length of database: 415
Effective search space:   176375
Effective search space used:   176375
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:

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