GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Phaeobacter inhibens BS107

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate GFF2135 PGA1_c21670 betaine aldehyde dehydrogenase BetB

Query= BRENDA::Q72IB9
         (516 letters)



>FitnessBrowser__Phaeo:GFF2135
          Length = 485

 Score =  235 bits (600), Expect = 2e-66
 Identities = 164/479 (34%), Positives = 236/479 (49%), Gaps = 17/479 (3%)

Query: 41  YIGGEWV-DTKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDRS 99
           +I GE+V DT    + +  +A  E + T   A  A  E AL  A  A K W      +R 
Sbjct: 12  FINGEYVEDTAGTPIPVIYAATGEQIATVHAATPAIVEQALSTAKAAQKAWARMTGTERG 71

Query: 100 RLLLKAAALMRRRKRELEATLVYEVGKNWVEAS-ADVAEAIDFIEYYARAALRYRYPAVE 158
           R+L +AA +MR R  +L     Y+ GK   E   AD     D +EY+   A        E
Sbjct: 72  RILRRAADIMRERNHDLSVLETYDTGKPLQETLVADATSGADALEYFGGLAASL---TGE 128

Query: 159 VVPYPGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVVGAK 218
            +P   +   +    LG  V I  WN+P  I        +A GN+++ KP+E   +   K
Sbjct: 129 HIPLGEDWVYTKREALGLCVGIGAWNYPTQIACWKGAPALACGNSMVFKPSETTPLCALK 188

Query: 219 VFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRLAPG 278
           V EI  EAG P GV N + G+GE VG  LV  PR   ++ TGS+  G K+Y AA      
Sbjct: 189 VAEILIEAGAPAGVFNVVQGMGE-VGGALVTDPRVDKVSLTGSVPTGKKVYAAAAE---- 243

Query: 279 QTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYEPV 338
               K   +E GGK  +I+ + AD D A  G +   +   GQ CS  +R+ + +G  E  
Sbjct: 244 --GMKHVTMELGGKSPLIIFDDADIDNAVGGAINGNFYSSGQVCSNGTRVFVQKGIKEKF 301

Query: 339 LERVLKRAERLSVG-PAEENPDLGPVVSAEQERKVLSYIEIGKNEG-QLVLGGKRLEGEG 396
           L R+ +R     +G P +E    GP+V+  Q   VL YIE GK EG +L+ GG+R + +G
Sbjct: 302 LARLAERTGNAILGDPMDEATSFGPMVTENQMNIVLGYIEKGKEEGARLICGGRRADMDG 361

Query: 397 YFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKREH 456
           YFI PTVF +V     IA+EEIFGPV+SV+      E +  ANDT +GL+ GV+++    
Sbjct: 362 YFIEPTVFADVTDDMTIAREEIFGPVMSVLDFDTEEEVVARANDTEFGLSAGVFTKDFTR 421

Query: 457 LEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAKTGALDYLRLFLEMKAVAER 515
                     G+ + N      +    PFGG K SG   +  + + ++ F ++K+V  R
Sbjct: 422 AHRVIGNLEAGSCFINSYNDAPVEA--PFGGVKASGV-GRENSKEAIKHFSQVKSVYVR 477


Lambda     K      H
   0.319    0.137    0.403 

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: 586
Number of extensions: 39
Number of successful extensions: 6
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: 516
Length of database: 485
Length adjustment: 34
Effective length of query: 482
Effective length of database: 451
Effective search space:   217382
Effective search space used:   217382
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