GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Caulobacter crescentus NA1000

Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized)
to candidate CCNA_02480 CCNA_02480 NAD-dependent benzaldehyde dehydrogenase II

Query= curated2:Q9K5Z5
         (515 letters)



>FitnessBrowser__Caulo:CCNA_02480
          Length = 487

 Score =  228 bits (582), Expect = 3e-64
 Identities = 144/451 (31%), Positives = 226/451 (50%), Gaps = 16/451 (3%)

Query: 52  IVSVNPAMKEQVIGVVSKASREIVDDAFKSAETAFHTWKNVNPEERANILIRAAAIIRRR 111
           +++V     E V+  V +A R  V  A  SA+ A   W  +  + R  IL+RAA ++   
Sbjct: 27  VIAVQEPATETVLTQVGRADRSDVARAAASAKAAQPAWAALTADARQAILLRAADLLVEH 86

Query: 112 KHEFSAWLVKEAGKPWKEADADTAEAIDFLEYYARQMITLKDGKPVNSREGEHNRYFYTP 171
             + + W+++E+G    +A  +   A  F+   A  M T   G  + S  G+ +     P
Sbjct: 87  APDLAPWIMRESGSVAAKAAVELEHAAGFVRQ-AGAMATEAAGLVLPSSPGKTSIARRVP 145

Query: 172 IGVCVTISPWNFALAIMAGTTVAPIVTGNTVLLKPASTTPVVAAKFV-EVLEEAGLPKGV 230
           +GV   ISP+NF L +        + TGN V+LKP   TP+     +  V E AGLP G+
Sbjct: 146 LGVVAVISPFNFPLVLSIRAVAPALATGNAVVLKPDPRTPISGGFLIARVFEAAGLPAGL 205

Query: 231 VNFVPGSGTDIGDYLIDHPKTSLITFTGSRDVGVRLYERAAVVHPGQQHLKRVIVEMGGK 290
           ++ +PG   + GD L   P  +++ FTGS   G ++ E A        HLK+V +E+GGK
Sbjct: 206 LHVLPGDA-EAGDALCRDPNIAMVAFTGSTGAGRKVGEVAGA------HLKKVALELGGK 258

Query: 291 DTVVVDKDADLDLAAQSIVTSAFGFSGQKCSAGSRAVIHQDVYDVVLEKAVALTKQLSVG 350
           + +++  DAD D+AA +    A+   GQ C    R ++ + ++D V+E+  A    L VG
Sbjct: 259 NPLIILDDADPDVAASNAAWGAWLHQGQVCMTAGRLLVQRGIHDAVVERLAAKAGHLPVG 318

Query: 351 EPTAPDVYMGPVVDQGAFSKIMSYIEVGKEEG-RLMVGGEGDDSKGFFIQPTIFADVDPH 409
           +P   DV +GP++ +G   ++ + +     +G RL+ GG     KG    PT+   V P 
Sbjct: 319 DPMRGDVALGPLISRGQLDRVHAIVSDTVADGARLVAGG---THKGLCYAPTVLTGVAPG 375

Query: 410 ARIMQEEIFGPVVAFSKARDFDHALEIANNTEYGLTGAVITTNRHHIEKAKRDFHVGNLY 469
            R  +EEIFGP+ A +   D D A  +AN+  YGL+  +I+ +            VG+L+
Sbjct: 376 MRAFEEEIFGPIAAVTVFDDLDEAARLANDGPYGLSAGIISGSVGRAMTLGAKLEVGHLH 435

Query: 470 FNRNCTGAIVGYH-PFGGFKMSGTDSKAGGP 499
            N     A  G H PFGG K SG  ++  GP
Sbjct: 436 INDQTVDA--GPHSPFGGMKASGNGTRISGP 464


Lambda     K      H
   0.318    0.135    0.394 

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: 606
Number of extensions: 27
Number of successful extensions: 7
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: 487
Length adjustment: 34
Effective length of query: 481
Effective length of database: 453
Effective search space:   217893
Effective search space used:   217893
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 (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