GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Dietzia timorensis ID05-A0528

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_006897513.1 BJL86_RS01995 aldehyde dehydrogenase

Query= BRENDA::Q9K9B2
         (515 letters)



>NCBI__GCF_001659785.1:WP_006897513.1
          Length = 493

 Score =  241 bits (614), Expect = 6e-68
 Identities = 158/490 (32%), Positives = 245/490 (50%), Gaps = 25/490 (5%)

Query: 37  YPLIINGERVTTEDKIQSWNPARKDQLVGSVSKANQDLAEKAIQSADEAFQT--WRNVNP 94
           Y L I+G+ V T++     +P     ++ +++K      + A+++A  AF +  WR    
Sbjct: 4   YSLFIDGKSVDTDETYDVVSPG-DGTVIATLAKGGTAEVDAAVEAAAAAFASSGWRETPM 62

Query: 95  EERANILVKAAAIIRRRKHEFSAWLVHEAGKPWKEADADTAEAIDFLEYYARQMIELNRG 154
            ERA ++ +AA  I  R  E S     E G P + A      ++ F   + R   +L R 
Sbjct: 63  HERAAVIDRAADAIEARAEEISLLASRENGTPVRLAQG---LSVGFPVMHIRYFADLAR- 118

Query: 155 KEILSRPGEQNRYFY-----TPMGVTVTISPWNFALAIMVGTAVAPIVTGNTVVLKPAST 209
           + +  +P   +          P+GV   I PWNF L + V  ++  I  GN+VVLK    
Sbjct: 119 RHVTDQPTMVSGSVVGIIRREPIGVVAGIVPWNFPLLLTVWKSIPAIAAGNSVVLKADEK 178

Query: 210 TPVVAAKFVEVLEDAGLPKGVINYVPGSGAEVGDYLVDHPKTSLITFTGSKDVGVRLYER 269
           TP  A    EVL+ AGLP GV N + G GAEVG +L  HPK   ++FTGS   G  +   
Sbjct: 179 TPSTALILAEVLKAAGLPDGVFNVITGDGAEVGGHLTKHPKVRKVSFTGSTATGRTVMAN 238

Query: 270 AAVVRPGQNHLKRVIVEMGGKDTVVVDRDADLDLAAESILVSAFGFSGQKCSAGSRAVIH 329
           AA        +K+V +E+GGK   +V  DADLDLA +  L +    +GQ C +G+R  +H
Sbjct: 239 AA------ERVKKVTMELGGKGANIVLPDADLDLAVDGSLWAFLVHAGQACESGTRLFVH 292

Query: 330 KDVYDEVLEKTVALAKNLTVGDPTNRDNYMGPVIDEKAFEKIMSYIEIGKKEGRLMTG-- 387
           + +Y E +++ V  A  LT+GDPT+    +GP+++    E++  +I+ GKK+G  +    
Sbjct: 293 RTIYREFVDRLVQRASQLTIGDPTDMSTDIGPLMNRAQRERVEGFIDSGKKDGATVAFQA 352

Query: 388 --GEGDSSTGFFIQPTIIADLDPEAVIMQEEIFGPVVAFSKANDFDHALEIANNTEYGLT 445
                 +  G ++ PTI  D+ P+  I  EEIFGPVV+    +D D  +  AN +EYGL+
Sbjct: 353 ELPADLNREGMWVPPTIFTDVTPDMKITTEEIFGPVVSVMAYDDIDAVVAEANTSEYGLS 412

Query: 446 GAVITRNRAHIEQAKREFHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAGGPDYLALH 505
             V T +             G ++ N     A+ G  PFGG K SG   +  GP+ +  +
Sbjct: 413 AGVWTTDYTVAMDLAHRLEAGTVWIND--WHALSGQLPFGGVKQSGF-GREMGPNAINEY 469

Query: 506 MQAKTVSEMY 515
              K+++  Y
Sbjct: 470 TNEKSIAIDY 479


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: 605
Number of extensions: 22
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: 515
Length of database: 493
Length adjustment: 34
Effective length of query: 481
Effective length of database: 459
Effective search space:   220779
Effective search space used:   220779
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 24 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