GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Paraburkholderia bryophila 376MFSha3.1

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate H281DRAFT_03016 H281DRAFT_03016 aldehyde dehydrogenase (acceptor)

Query= BRENDA::Q9K9B2
         (515 letters)



>FitnessBrowser__Burk376:H281DRAFT_03016
          Length = 483

 Score =  274 bits (701), Expect = 5e-78
 Identities = 168/471 (35%), Positives = 255/471 (54%), Gaps = 22/471 (4%)

Query: 35  KEYPLIINGERVT--TEDKIQSWNPARKDQLVGSVSKANQDLAEKAIQSADEAFQTWRNV 92
           + + L+I+G+R+   T +   + NPA ++  +  V++ +    + A+++A  A + W  +
Sbjct: 8   RRHDLLIDGKRLPPGTGEYSVNINPATEEP-IAHVAQGSAADVDTAVRAARAALKVWNGI 66

Query: 93  NPEERANILVKAAAIIRRRKHEFSAWLVHEAGKPWKEA-DADTAEAIDFLEYYARQMIEL 151
              ER  IL + A ++R    E +A    +AGKP       D   AID LEYYA    ++
Sbjct: 67  KAAERGRILSRLAGLMRANLDELAALESLDAGKPIAAVMRQDVPAAIDTLEYYAGWCDKI 126

Query: 152 NRGKEILSRPGEQNRYFYTPMGVTVTISPWNFALAIMVGTAVAPIVTGNTVVLKPASTTP 211
           N G+ +  RP         P+GV   I PWNF L I +      +  G T+++KPA  TP
Sbjct: 127 N-GQVVPVRPDALTYTLREPVGVVAAIVPWNFPLMIGMWKIAPALACGCTLIVKPAEITP 185

Query: 212 VVAAKFVEVLEDAGLPKGVINYVPGSGAEVGDYLVDHPKTSLITFTGSKDVGVRLYERAA 271
           + A +  E+  +AG+P GV+N V G G  VGD LV HP    +TFTGS  VG  + + AA
Sbjct: 186 LSALRIGELALEAGVPPGVLNIVTGKGRVVGDALVAHPGVDKVTFTGSPSVGRGILQGAA 245

Query: 272 VVRPGQNHLKRVIVEMGGKDTVVVDRDADLDLAAESILVSAFGFSGQKCSAGSRAVIHKD 331
                  + KRV +E+GGK   ++  DA+LD A  +     F  +GQ CSAGSR + H+D
Sbjct: 246 ------GNFKRVTLELGGKSANLIFPDANLDNAVRAAASGIFFNTGQVCSAGSRILAHRD 299

Query: 332 VYDEVLEKTVALAKNLTVGDPTNRDNYMGPVIDEKAFEKIMSYIEIGKKEG-RLMTGGEG 390
           VYDEV+E+  A AK++ VGDP++R+  MGP+I     + ++ Y++ G+ EG  L+TGG  
Sbjct: 300 VYDEVVERLAARAKSIKVGDPSSRETSMGPLISAAQMKTVLGYVDAGRSEGASLVTGGGR 359

Query: 391 DSSTGFFIQPTIIADLDPEAVIMQEEIFGPVVAFSKANDFDHALEIANNTEYGLTGAVIT 450
               GFF++PT+ A+++ E  I QEEIFGPV +  + ND   A+ IAN T Y L   V +
Sbjct: 360 IGERGFFVEPTVFANVEHEMRISQEEIFGPVASVIRFNDEADAIRIANGTLYSLAAGVWS 419

Query: 451 RNRAHIEQAKREFHVGNLYFNRNCTGAIVGYH----PFGGFKMSGTDSKAG 497
            +   + +  R+   G ++ N        GY     P+GG   SG   + G
Sbjct: 420 ADIGRVHRVARDLRAGTVWIN------TYGYTDVRLPWGGSGDSGFGREHG 464


Lambda     K      H
   0.316    0.134    0.388 

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: 578
Number of extensions: 19
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: 483
Length adjustment: 34
Effective length of query: 481
Effective length of database: 449
Effective search space:   215969
Effective search space used:   215969
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