GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh in Caulobacter crescentus NA1000

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate CCNA_00618 CCNA_00618 succinylglutamic semialdehyde dehydrogenase

Query= BRENDA::P76217
         (492 letters)



>lcl|FitnessBrowser__Caulo:CCNA_00618 CCNA_00618 succinylglutamic
           semialdehyde dehydrogenase
          Length = 472

 Score =  490 bits (1261), Expect = e-143
 Identities = 254/471 (53%), Positives = 321/471 (68%), Gaps = 4/471 (0%)

Query: 15  ASR-VKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAERHAVVERFAALLE 73
           ASR + R+P +GE +      DA  ++ AC +ARAAF  WA    AER A+  RFA  + 
Sbjct: 3   ASRLISRDPYTGEAIADFAVNDARSIDAACHSARAAFAEWAMTPLAERRAIALRFAETVR 62

Query: 74  SNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQRSEMPDGAASLRHR 133
           + + E+  +IARETGKP WEA TE  ++  K+AISI+A   R GE+   M D  A L HR
Sbjct: 63  ARREEIATLIARETGKPMWEALTEADSVAAKVAISIRAQDERAGERSEPMADATARLAHR 122

Query: 134 PHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAVMRLWQQAGLPPGV 193
           PHGVLAV GP+NFP HL NGHIVPALLAGN ++FKPSE TP  G+ +  LW+ AGLP  V
Sbjct: 123 PHGVLAVIGPFNFPMHLANGHIVPALLAGNAVVFKPSEKTPACGQLMGELWRAAGLPDHV 182

Query: 194 LNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKILALEMGGNNPLIID 253
           L +V GG E G+AL   E LDG+LFTG    G  +HR L+  P KILALE+GGN PL++ 
Sbjct: 183 LTIVIGGGEAGEALVRHEALDGVLFTGGVQAGRAIHRALADAPHKILALELGGNAPLVVW 242

Query: 254 EVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVAVSQRLTPGNWDDE 313
           +VADI+AA HL +QSA+VTAGQRCTCARRL+L  GA+GDA L  L  +  RL  G     
Sbjct: 243 DVADIEAAAHLIVQSAYVTAGQRCTCARRLILPEGARGDALLEALTMLMDRLVIGGPFQS 302

Query: 314 PQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSLLTPGIIEMTGVAGVPD 373
           P PF+G +I   AA QV+ A  ++ A GGRPL    + +A ++LL+PG+IE+T  A + D
Sbjct: 303 PAPFMGPVIDAHAAAQVLAAQDRMTADGGRPLRLAAVREARSALLSPGLIELTD-APLRD 361

Query: 374 EEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLLEARAGIVNWNKPL 433
           EE+FGPLL+V R   FD A+ +AN TRFGL+ GL+S +   + +     RAGIVNWN+P 
Sbjct: 362 EEIFGPLLQVRRAADFDAALALANATRFGLAAGLISDDEALYRRFWTSVRAGIVNWNRPT 421

Query: 434 TGAASTAPFGGIGASGNHRPSAWYAADYCAWPMASLESDS--LTLPATLNP 482
           TGA+S APFGG+G SGNHRPSA+YAADY A+P+A LES S    LP  LNP
Sbjct: 422 TGASSAAPFGGVGGSGNHRPSAYYAADYSAYPVAGLESPSPVYRLPIGLNP 472


Lambda     K      H
   0.318    0.134    0.412 

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: 718
Number of extensions: 27
Number of successful extensions: 2
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: 492
Length of database: 472
Length adjustment: 34
Effective length of query: 458
Effective length of database: 438
Effective search space:   200604
Effective search space used:   200604
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 (21.7 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, 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