GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Pseudomonas fluorescens GW456-L13

Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate PfGW456L13_2690 Aldehyde dehydrogenase (EC 1.2.1.3)

Query= SwissProt::P94391
         (515 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2690
          Length = 502

 Score =  260 bits (665), Expect = 7e-74
 Identities = 167/481 (34%), Positives = 245/481 (50%), Gaps = 20/481 (4%)

Query: 32  YLGKDYPLVINGERVE-TEAKIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFE--E 88
           +LGK   + I G  VE ++ +   +     E ++ R+   + +  ++A+QAA   F+   
Sbjct: 21  FLGKVQKMFIGGAWVEASDGQTSDVVEPSTEGLITRIPMGTTDDLDRAVQAARAQFDGGA 80

Query: 89  WRYTSPEERAAVLFRAAAKVRRRKHEFSALLVKEAGKPWNEA-DADTAEAIDFMEYYARQ 147
           WR   P ER  ++ R A  + +   E + +   + GK    A D D    +D + Y+A  
Sbjct: 81  WRQAKPAERERMMQRLADLIEQNAAELAQIESIDMGKSVAFAKDVDIQGTVDTLRYFAGW 140

Query: 148 MIELAKGKPVNSREGEKNQYVYT---PTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVL 204
             +L       S  G  N   YT     GV   I PWNF    MA    A + TG TVV+
Sbjct: 141 ATKLHGRTVEPSLPG--NYLAYTRKEAVGVVGAIVPWNFPLQTMAWKLGAALATGCTVVV 198

Query: 205 KPASATPVIAAKFVEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGT 264
           KPA  T + A +F E+++E+G+P GV+N V G G+ VG  +  HP    +TFTGS  VG 
Sbjct: 199 KPAELTSLSALRFAELVQEAGIPDGVINIVTGRGSVVGAAMATHPGIDKLTFTGSTPVGQ 258

Query: 265 RIFERAAKVQPGQQHLKRVIAEMGGKDTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGS 324
            +   A         +KR+  E+GGK  V+V  DADI  AAQ++    F  +GQ C AG+
Sbjct: 259 TVGRAAL------DDMKRLTLELGGKSPVIVCADADIPAAAQAVANGVFFNSGQVCDAGT 312

Query: 325 RAVVHEKVYDQVLERVIEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEG-R 383
           RA +H  VYD+ L  +I  T +   A     D ++GP++      ++  YIE GK EG  
Sbjct: 313 RAYIHSSVYDEFLRELITYTRTLKMAPGLDPDCFIGPLVSALQKQRVTEYIETGKAEGAE 372

Query: 384 LVSGGTGDDSKGYFIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYG 443
           LV GG   D  G+F++PTIFA+     R++QEEIFGPV+      D +EAL +AN++ YG
Sbjct: 373 LVYGGQPVDGPGFFVEPTIFANCRNDMRIVQEEIFGPVLVTAPFDDEEEALALANDSPYG 432

Query: 444 LTGAVITNNRKHIERAKQEFHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAGGP--DY 501
           L  A+ +N+   +         G++Y N +  G +    PFGG+K SG     G    DY
Sbjct: 433 LAAALYSNDLGKVHSLIPRLKAGSVYVNAH--GTLDPSMPFGGYKQSGFGKDLGAEQLDY 490

Query: 502 L 502
           L
Sbjct: 491 L 491


Lambda     K      H
   0.316    0.133    0.379 

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: 612
Number of extensions: 29
Number of successful extensions: 5
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: 515
Length of database: 502
Length adjustment: 34
Effective length of query: 481
Effective length of database: 468
Effective search space:   225108
Effective search space used:   225108
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 (21.6 bits)
S2: 52 (24.6 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