GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Herbaspirillum seropedicae SmR1

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate HSERO_RS22910 HSERO_RS22910 benzaldehyde dehydrogenase

Query= curated2:A8A0T8
         (492 letters)



>FitnessBrowser__HerbieS:HSERO_RS22910
          Length = 487

 Score =  203 bits (516), Expect = 1e-56
 Identities = 153/482 (31%), Positives = 236/482 (48%), Gaps = 25/482 (5%)

Query: 7   GDWITG-QGASRVKRNPVSGEVLWQGNDAGAAQVEQACRAARAAFPRWARLSLAERQVVV 65
           G W+   QGA+ ++  P +G  L Q   A    V  +   A AA   W  +   ER  + 
Sbjct: 19  GQWVAAAQGATVLE--PATGRPLTQVGLASPDDVSASVELAIAAQAAWVAMPPRERADIF 76

Query: 66  ERFAGLLESNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQRSEMPD 125
            R AGL   +  EL  ++ARETG   ++   EV   I    ++        G+     P 
Sbjct: 77  RRAAGLFHQHFDELARMVARETGGVLFKGEHEVREAITLCHLAAGMPLQAQGQLLPSTPG 136

Query: 126 GAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAVM-RLW 184
             +  R  P GV+ V  P+NFP  L    + PAL AGN ++ KP   TP SG  ++ R++
Sbjct: 137 RLSIARRAPLGVIGVISPFNFPLILTLRTVAPALAAGNAVVVKPDLRTPVSGGFMLARIF 196

Query: 185 QQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKILALEM 244
           +QAGLP G+L+++ GG ETG+AL     +  + FTGS   G ++  +L+G+  K L+LE+
Sbjct: 197 EQAGLPAGLLHVLPGGAETGEALVTAPGVPMIAFTGSPAVGRRIG-ELAGRHLKKLSLEL 255

Query: 245 GGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVAVSQR 304
           GG N L+I E AD+D A       A++  GQ C  A R+L+ +  + +  L RL   ++ 
Sbjct: 256 GGANALVILEDADLDVAASHAAWGAWLHQGQICMAANRILVHASLE-EGLLQRLADKARH 314

Query: 305 LTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRTLLAPR---LLQSETSL--LT 359
           L  G+     Q  +G +I E+  Q+V    Q+  A G + +   R   L    T L  + 
Sbjct: 315 LPVGD-GASGQVALGPMIDERQLQRVHALVQESVAAGAQLVAGGRYEQLFYQPTVLGGVR 373

Query: 360 PGIIEMTGVAGVPDEEVFGPLLRVWRYDSFEEAILMANNTRFGLSCGLVSPEREKFDQLL 419
           PG+        V +EE+FGP+  V R+D+ E+AI +AN    GL+ G++SP   +   + 
Sbjct: 374 PGM-------RVFEEEIFGPVASVIRFDNDEDAIALANRHAGGLAAGVLSPSVGRAMAVA 426

Query: 420 LEARAGIVNWNKPLTGAASTAPFGGIGASGNHR----PSAWYAADYCAWPMASLESDSLT 475
              R G+V+ N          PFGG G +GN      P+ W   +Y  W   ++   ++ 
Sbjct: 427 ARLRQGMVHVNDQTVNDECVNPFGGPGIAGNGASVGGPADW--EEYTQWRWTTIRQQAMP 484

Query: 476 LP 477
            P
Sbjct: 485 YP 486


Lambda     K      H
   0.318    0.134    0.408 

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: 687
Number of extensions: 44
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: 492
Length of database: 487
Length adjustment: 34
Effective length of query: 458
Effective length of database: 453
Effective search space:   207474
Effective search space used:   207474
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