GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Algiphilus aromaticivorans DG1253

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_052367856.1 U743_RS09915 aldehyde dehydrogenase family protein

Query= BRENDA::Q9RW56
         (523 letters)



>NCBI__GCF_000733765.1:WP_052367856.1
          Length = 539

 Score =  176 bits (446), Expect = 2e-48
 Identities = 143/474 (30%), Positives = 219/474 (46%), Gaps = 21/474 (4%)

Query: 54  KIQSINPCDTSEVVGTTAKATIGDAENALQGAWKAFESWKKWDMDARARILLKAAAILKR 113
           +I   NP  T E +GT   AT  + + A++ A  A + W +     R  +L +    +  
Sbjct: 19  EIDCRNPA-TGETLGTLPAATPAEVQEAVERARAAQKQWAQSSFRQRRAVLRRMLQSILD 77

Query: 114 RRLEACALMSIEVGKNYAEADV-EVAEAIDFLEYYARSAMKYAGFGSSETTWFEGEENGL 172
              E CA +  + GK +  A + EV    + + +  R   K+    S  +   + ++  +
Sbjct: 78  DVDELCAAVVADSGKTWENALLGEVMPVCNKIRWIIRYGEKHLRSESVPSGLLKHKKGRI 137

Query: 173 MSIPLGVGVSISPWNFPCAIFVGMAAAPIVAGNCVVVKPAEDAGLIAGFMVDILREA--- 229
              PLGV   I PWN+P     G   AP++AGN VV+K +E           +  EA   
Sbjct: 138 EYRPLGVVACIVPWNYPFQNIFGSLVAPLMAGNAVVLKASEAVAWSTQRFRRVFEEALVA 197

Query: 230 -GLPAGVLQFLPGVGKEVGEYLTTHAKTRFITFTGSRAVGLHINEVAAKVQPGQKWIKRV 288
            G PA  +Q + G G E G  L   ++ + I F GS   G  I E +A+       +  V
Sbjct: 198 EGFPAETVQIINGYG-ETGAALV-RSRVQKILFIGSVGNGRKIIEGSAE------HLTPV 249

Query: 289 IMELGGKDGLIVDETADIENAITAATQGAFGFNGQKCSAMSRLIVVDSVYDEVVNGFVER 348
           +MELGGKD +I+ + A +E A+ +A  G F   GQ C A  RLIV   ++D  V      
Sbjct: 250 VMELGGKDPMIICDDAHLEQAVHSALSGCFINLGQNCIASERLIVQAGIFDRFVEEVTRI 309

Query: 349 AKALKMGTGEE--NANVTAVVNQMSFNKIKGYLELAPSEG-KVLLGGEATGEANGKQGYY 405
           A  ++ G  E+    +V A+        +   +  A + G + L+GG       G  G +
Sbjct: 310 AGDMRQGVPEQPGTLDVGAMTTPQQVRIVDELVRDALASGARALVGGRLP---EGASGSF 366

Query: 406 IQPTIVGDVDRNSRLAQEEIFGPVVAVLRAKDWQDALDIANSTEYGLTGGVCSNSRERLE 465
             PT++ DV    R+A+EE+FGPV+ ++RA D  +A+ IAN+ ++GL   V S  R+R E
Sbjct: 367 YPPTVLVDVTPEMRIAREEVFGPVMLIMRAADDAEAVRIANAIDFGLQSSVFSRDRKRAE 426

Query: 466 QARAEFEVGNLYFNRKITGAIVGVQPFGGYNMSGTDSKAGGPDYLSNFMQLKTV 519
           +  AE E G    N      +    PFGG   SG   +  G D L  +   K V
Sbjct: 427 RIAAELEAGATCINDFGLCYLNQDLPFGGVKYSGF-GRMNGRDGLRAYTNPKAV 479


Lambda     K      H
   0.317    0.134    0.391 

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: 621
Number of extensions: 34
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: 523
Length of database: 539
Length adjustment: 35
Effective length of query: 488
Effective length of database: 504
Effective search space:   245952
Effective search space used:   245952
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