GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Dyella japonica UNC79MFTsu3.2

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate N515DRAFT_3729 N515DRAFT_3729 aminomuconate-semialdehyde/2-hydroxymuconate-6-semialdehyde dehydrogenase

Query= BRENDA::Q72IB9
         (516 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3729
          Length = 483

 Score =  231 bits (588), Expect = 6e-65
 Identities = 174/480 (36%), Positives = 247/480 (51%), Gaps = 28/480 (5%)

Query: 50  KERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDRSRLLLKAAALM 109
           +ER + +   A  EV     ++  A+ +AA+ AA  A   W   P E R+RLL + A L+
Sbjct: 19  QERWLEVFEPATGEVFAHCPESSFADVDAAVAAAVAAAPGWAATPSEQRARLLQRLADLI 78

Query: 110 RRRKRELEATLVYEVGKNWVEA-SADVAEAIDFIEYYARAALRYRYP--AVEVVPYPGED 166
             R  E  A    + GK    A S D+  A+  + Y+A A + +     A+E+    G  
Sbjct: 79  EARLDEFAALESRDSGKPLSLARSLDIPRAVSNLRYFAAAIVPWSSESHAMEL----GAI 134

Query: 167 NESFYVPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVVGAKVFEIFHEA 226
           N +   PLG    I+PWN P+ +FT  I   +A GN V+AKP+E      A + E+  EA
Sbjct: 135 NYTLRQPLGVVACISPWNLPLYLFTWKIAPALAAGNAVVAKPSEITPCTAALLGELSIEA 194

Query: 227 GFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRLAPGQTWFKRAY 286
           GFPPGV+N + G G EVG  LVEH   + ++FTGS   G +I  AA   AP    FK+  
Sbjct: 195 GFPPGVLNIVQGRGPEVGQALVEHRDVKAVSFTGSTRTGAQIAAAA---APR---FKKLS 248

Query: 287 VETGGKDAIIVDETADF-DLAAEGVVVSAYGFQGQKCSAASRLILTQGAYEPVLERVLKR 345
           +E GGK+  IV   AD  D   + +V S +  QG+ C   SRL++ +  Y+   ER L +
Sbjct: 249 LELGGKNPAIVFADADLSDANLDTIVRSGFANQGEICLCGSRLLVQRSIYDAFRERYLAK 308

Query: 346 AERLSVG-PAEENPDLGPVVSAEQERKVLSYIEIGKNEGQLVL-GGKRLE-----GEGYF 398
              L VG P E   DLG +VS E   KV   I   + EG  VL GG  L        G++
Sbjct: 309 VRALRVGDPREAATDLGALVSREHFDKVTGCIAQARAEGGRVLCGGDALALPGPLAGGWY 368

Query: 399 IAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSR--KREH 456
           +APTV   + P+    Q+EIFGPV+++I   D A+AL +AN T YGL   +++    R H
Sbjct: 369 VAPTVIEGLGPETATNQQEIFGPVVTLIPFDDEAQALAIANGTGYGLAASLWTTDLSRAH 428

Query: 457 LEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAKTGALDYLRLFLEMKAVAERF 516
              A+ +F  G ++ N  +   L    PFGG K SG   + G ++ LR F E K +  R+
Sbjct: 429 RFGAQLDF--GIVWINCWLLRDL--RTPFGGAKQSGV-GREGGVEALRFFTEPKNICIRY 483


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: 565
Number of extensions: 31
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: 516
Length of database: 483
Length adjustment: 34
Effective length of query: 482
Effective length of database: 449
Effective search space:   216418
Effective search space used:   216418
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