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_082908505.1 BJL86_RS03515 aldehyde dehydrogenase

Query= BRENDA::Q9RW56
         (523 letters)



>NCBI__GCF_001659785.1:WP_082908505.1
          Length = 507

 Score =  201 bits (510), Expect = 7e-56
 Identities = 159/515 (30%), Positives = 251/515 (48%), Gaps = 38/515 (7%)

Query: 19  ENVQAYQAALAKVRKELLGKHYPLIIDGQEVDTEG--KIQSINPCDTSEVVGTTAKATIG 76
           E V    +AL+    + + +H  L I GQ  +  G  KI  ++P ++ E +G+   A   
Sbjct: 15  EEVPTLSSALSD---QAVTEHSTLFIGGQWREPNGREKITVVSP-NSGEEIGSVPLANRA 70

Query: 77  DAENALQGAWKAFES---WKKWDMDARARILLKAAAILKRRRLEACALMSIEVGKNYAEA 133
           D + A+  A +AF+    W   +   RA  L + A  L+ R  +  +L+S + G     A
Sbjct: 71  DIDAAVATARQAFDDPSVWSGLEPAERAAHLRRFADELEARGEKIASLVSSQNGMPVTIA 130

Query: 134 -DVEVAEAIDFLEYYARSAMKYAGFGSSETTWFEGEENGLMSI---PLGVGVSISPWNFP 189
             +E       L YY+    K            EG   G++ +   P+GV  +I PWN+P
Sbjct: 131 GQMEAVYPATLLRYYSDLIEKQT------PDLREGMMGGVVEVQRQPIGVVGAIVPWNYP 184

Query: 190 CAIFVGMAAAPIVAGNCVVVKPAEDAGLIAGFMVDILREAGLPAGVLQFLPGVGKEVGEY 249
            ++     A  + AG  +V+KP+ +  L +  + +    AGLPAGV+  +PG G++ G Y
Sbjct: 185 QSLAAFKYAPALAAGCTMVIKPSPETVLDSVVLAEAAEAAGLPAGVVNIVPG-GRDEGAY 243

Query: 250 LTTHAKTRFITFTGSRAVGLHINEVAAKVQPGQKWIKRVIMELGGKDGLIV--DETADIE 307
           L  HA    + FTGS A G  I EV  ++      ++ V +ELGGK   IV  D   D+E
Sbjct: 244 LVEHADIDKVAFTGSTAAGKKIAEVCGRL------LRPVTLELGGKSASIVLDDAELDLE 297

Query: 308 NAITAATQGAFGFNGQKCSAMSRLIVVDSVYDEVVNGFVERAKALKMGTGEENAN-VTAV 366
                        NGQ C   +R++   S Y EVV+     A ++ +G   + A  +  +
Sbjct: 298 TIGNDLFVSTLVNNGQTCFLGTRVLAPKSRYGEVVDALTAFAGSMAVGDSLDPATQIGPM 357

Query: 367 VNQMSFNKIKGYLELAPSEG-KVLLGGEATGEANGKQG-YYIQPTIVGDVDRNSRLAQEE 424
             Q    +++GY+E   SEG ++  GG   G   G+ G +++ PT+  DV+ +  +A+EE
Sbjct: 358 ATQTHLGRVEGYIEKGRSEGGRITTGG---GRPEGRDGGWFVSPTVFADVNNSDTIAREE 414

Query: 425 IFGPVVAVLRAKDWQDALDIANSTEYGLTGGVCSNSRERLEQARAEFEVGNLYFNRKITG 484
           IFGPV++V++  D  DA+ IAN +EYGL G V S+  ER     +    G +  NR I  
Sbjct: 415 IFGPVLSVIQYDDDADAVRIANESEYGLGGTVWSSDPERARSVASRVNTGTIGINRYIPD 474

Query: 485 AIVGVQPFGGYNMSGTDSKAGGPDYLSNFMQLKTV 519
               V PFGG   SG   +  GP+ L+ +  LK++
Sbjct: 475 P---VAPFGGVKHSGMGREL-GPEGLAAYQNLKSI 505


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: 562
Number of extensions: 24
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: 523
Length of database: 507
Length adjustment: 35
Effective length of query: 488
Effective length of database: 472
Effective search space:   230336
Effective search space used:   230336
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