GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pad-dh in Pseudomonas fluorescens FW300-N2C3

Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate AO356_25485 AO356_25485 aldehyde dehydrogenase

Query= BRENDA::P80668
         (499 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_25485 AO356_25485 aldehyde
           dehydrogenase
          Length = 495

 Score =  444 bits (1143), Expect = e-129
 Identities = 231/495 (46%), Positives = 315/495 (63%), Gaps = 4/495 (0%)

Query: 6   VAVLSQVQQFLDRQHGLYIDGRPGPAQSEKRLAIFDPATGQEIASTADANEADVDNAVMS 65
           +A+L QV+ FL R+H L+IDG    +QS + L + +PATGQ IA  +DA+ +D+D AV S
Sbjct: 4   IALLPQVEAFLGRRHALFIDGGYVESQSRQTLDVVNPATGQVIAQVSDASPSDIDAAVES 63

Query: 66  AWRAFVSRRWAGRLPAERERILLRFADLVEQHSEELAQLETLEQGKSIAISRAFEVGCTL 125
           + R F  ++W+   PA R  +LL+ ADL+E++ EELAQ+ET + GK I ISRAFEV    
Sbjct: 64  SRRGF--KQWSQTAPAVRGHVLLKLADLLERNREELAQIETCQSGKIIHISRAFEVDQAA 121

Query: 126 NWMRYTAGLTTKIAGKTLDLSIPLPQGARYQAWTRKEPVGVVAGIVPWNFPLMIGMWKVM 185
           +++RY AG  TKI G+T+  S+P   G RY A+T +EPVGVV GIVPWNF  MI +WK+ 
Sbjct: 122 HFLRYYAGWATKINGETITPSLPSFAGERYTAFTLREPVGVVVGIVPWNFSTMIAIWKLA 181

Query: 186 PALAAGCSIVIKPSETTPLTMLRVAELASEAGIPDGVFNVVTGSGAVCGAALTSHPHVAK 245
            AL  GCS++IKPSE TPLT+LR+AELA EAG+P G  NV+TG G V G  L  HP   K
Sbjct: 182 SALVTGCSVIIKPSEFTPLTILRIAELAMEAGLPAGALNVLTGGGQV-GKGLIEHPGTNK 240

Query: 246 ISFTGSTATGKGIARTAADH-LTRVTLELGGKNPAIVLKDADPQWVIEGLMTGSFLNQGQ 304
           +SFTGS  TG  + + A    LTR TLELGGKN A  L+D DP+  + G++   FL+ GQ
Sbjct: 241 VSFTGSVPTGLAVGQAAMGAGLTRATLELGGKNAAGFLRDIDPEVAVNGIIEAGFLHSGQ 300

Query: 305 VCAASSRIYIEAPLFDTLVSGFEQAVKSLQVGPGMSPVAQINPLVSRAHCDKVCSFLDDA 364
           +CAA+ R ++     ++++    Q +  L +G  +    +  P+ +R H  K+  F   A
Sbjct: 301 ICAAAERFFVHRSQIESIMDKLAQRLSKLTIGSPLDERTEFGPVTNRQHQHKLAEFFAKA 360

Query: 365 QAQQAELIRGSNGPAGEGYYVAPTLVVNPDAKLRLTREEVFGPVVNLVRVADGEEALQLA 424
           +AQ   +I G     G G YV PT+++       L  EE FGP+         EE L+L 
Sbjct: 361 RAQNNTIIHGGKLIDGPGCYVEPTIILANRRDDALLNEETFGPIATFFPYDTEEELLELM 420

Query: 425 NDTEYGLTASVWTQNLSQALEYSDRLQAGTVWVNSHTLIDANLPFGGMKQSGTGRDFGPD 484
           NDT YGL+AS+WT +L +AL     ++AGTVWVN HTL+D  +PFGG K SG GR+FG  
Sbjct: 421 NDTPYGLSASLWTNDLGKALRMVPAIEAGTVWVNMHTLLDPAVPFGGSKSSGVGREFGSA 480

Query: 485 WLDGWCETKSVCVRY 499
           ++D + E KSV +RY
Sbjct: 481 FIDDYTELKSVMIRY 495


Lambda     K      H
   0.318    0.133    0.402 

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: 662
Number of extensions: 31
Number of successful extensions: 4
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: 499
Length of database: 495
Length adjustment: 34
Effective length of query: 465
Effective length of database: 461
Effective search space:   214365
Effective search space used:   214365
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: 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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