GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Caulo:CCNA_00618
          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 (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