GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Azospirillum brasilense Sp245

Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized)
to candidate AZOBR_RS09720 AZOBR_RS09720 succinate-semialdehyde dehdyrogenase

Query= BRENDA::P25526
         (482 letters)



>FitnessBrowser__azobra:AZOBR_RS09720
          Length = 497

 Score =  701 bits (1810), Expect = 0.0
 Identities = 342/480 (71%), Positives = 403/480 (83%), Gaps = 1/480 (0%)

Query: 3   LNDSNLFRQQALINGEWLDANNGEAIDVTNPANGDKLGSVPKMGADETRAAIDAANRALP 62
           L D+ L R Q  ++G W+DA++G+ ++VTNPA+G  LGSVP MGADETR AI+AA RA P
Sbjct: 14  LKDAELLRFQGFVDGRWIDADSGKTVEVTNPADGSVLGSVPMMGADETRRAIEAAERAWP 73

Query: 63  AWRALTAKERATILRNWFNLMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFAEE 122
           AWRALTAKERA  LR WF+LMM +Q+D+AR+MT EQGKPLAEA+GE++YAASFIEWFAEE
Sbjct: 74  AWRALTAKERAKTLRTWFDLMMANQEDIARIMTAEQGKPLAEARGEVAYAASFIEWFAEE 133

Query: 123 GKRIYGDTIPGHQADKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPA 182
           GKR+YGDTIP H   +R++V K+PIGVTAAITPWNFPAAMITRKAGPALAAGC MV+KPA
Sbjct: 134 GKRVYGDTIPQHLPGRRIVVTKEPIGVTAAITPWNFPAAMITRKAGPALAAGCPMVIKPA 193

Query: 183 SQTPFSALALAELAIRAGVPAGVFNVVTGSAGAVGNELTSNPLVRKLSFTGSTEIGRQLM 242
           + TP +ALA+A LA RAG+PAG+ +VVTGSA A+G E+T NP VRKL+FTGSTEIG++LM
Sbjct: 194 TATPLTALAMAVLAERAGIPAGILSVVTGSARAIGGEMTGNPTVRKLTFTGSTEIGKELM 253

Query: 243 EQCAKDIKKVSLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQDGVY 302
            QCA  +KKVSLELGGNAPF+VF+DADLD+AV+GA+ASK+RN GQTCVCANRL VQ GVY
Sbjct: 254 AQCAGTVKKVSLELGGNAPFLVFNDADLDEAVKGAIASKYRNTGQTCVCANRLLVQSGVY 313

Query: 303 DRFAEKLQQAVSKLHIGDGL-DNGVTIGPLIDEKAVAKVEEHIADALEKGARVVCGGKAH 361
           D FA KL +AV  L +G GL   G   GPLID  AV KVE+HI DA EKGARVV GGK H
Sbjct: 314 DAFAAKLAEAVKALKVGPGLTTEGAQQGPLIDMAAVEKVEDHIRDATEKGARVVLGGKRH 373

Query: 362 ERGGNFFQPTILVDVPANAKVSKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFYAR 421
           E GG+FF+PTIL DV    KV++EETFGP+APLFRF+ E + +  AN TEFGLAAYFY+R
Sbjct: 374 ELGGSFFEPTILADVTPAMKVAREETFGPVAPLFRFETEEEAVRMANATEFGLAAYFYSR 433

Query: 422 DLSRVFRVGEALEYGIVGINTGIISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYMCIG 481
           D+ RV+RV EALEYGIVGIN GIIS EVAPFGG+K SG+GREGSKYGIEDYLEIKY+C+G
Sbjct: 434 DIGRVWRVAEALEYGIVGINEGIISTEVAPFGGMKESGIGREGSKYGIEDYLEIKYLCMG 493


Lambda     K      H
   0.318    0.135    0.395 

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: 776
Number of extensions: 20
Number of successful extensions: 2
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: 482
Length of database: 497
Length adjustment: 34
Effective length of query: 448
Effective length of database: 463
Effective search space:   207424
Effective search space used:   207424
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