GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Azospirillum brasilense Sp245

Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate AZOBR_RS09720 AZOBR_RS09720 succinate-semialdehyde dehdyrogenase

Query= SwissProt::Q9I6M5
         (483 letters)



>FitnessBrowser__azobra:AZOBR_RS09720
          Length = 497

 Score =  711 bits (1836), Expect = 0.0
 Identities = 346/482 (71%), Positives = 405/482 (84%), Gaps = 1/482 (0%)

Query: 3   LKDAKLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALP 62
           LKDA+L R Q +VDG W+DAD+G+T++V NPA G ++GSVP MGA ETRRAIEAA++A P
Sbjct: 14  LKDAELLRFQGFVDGRWIDADSGKTVEVTNPADGSVLGSVPMMGADETRRAIEAAERAWP 73

Query: 63  AWRALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFGEE 122
           AWRALTAKERA  LR WFDLM+ NQ+D+AR+MT EQGKPLAEA+GE+AYAASF+EWF EE
Sbjct: 74  AWRALTAKERAKTLRTWFDLMMANQEDIARIMTAEQGKPLAEARGEVAYAASFIEWFAEE 133

Query: 123 AKRIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPA 182
            KR+YGDTIP H P +RI+V K+PIGVTAAITPWNFP+AMITRKAGPALAAGC MV+KPA
Sbjct: 134 GKRVYGDTIPQHLPGRRIVVTKEPIGVTAAITPWNFPAAMITRKAGPALAAGCPMVIKPA 193

Query: 183 SQTPYSALALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQLM 242
           + TP +ALA+A LAERAGIP G+ SVVTGSA  +GGE+T NP VRKLTFTGSTEIG++LM
Sbjct: 194 TATPLTALAMAVLAERAGIPAGILSVVTGSARAIGGEMTGNPTVRKLTFTGSTEIGKELM 253

Query: 243 AECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVY 302
           A+CA  +KKVSLELGGNAPF+VF+DADLD AV+GA+ SKYRN GQTCVCANRL VQ GVY
Sbjct: 254 AQCAGTVKKVSLELGGNAPFLVFNDADLDEAVKGAIASKYRNTGQTCVCANRLLVQSGVY 313

Query: 303 DAFVDKLKAAVAKLNIGNGLEA-GVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPH 361
           DAF  KL  AV  L +G GL   G   GPLID  AV KVE+HI DA  KGA+VV GGK H
Sbjct: 314 DAFAAKLAEAVKALKVGPGLTTEGAQQGPLIDMAAVEKVEDHIRDATEKGARVVLGGKRH 373

Query: 362 ALGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYAR 421
            LGG+FFEPTIL DV     V+++ETFGP+AP+FRF+ E E + M+N TEFGLA+YFY+R
Sbjct: 374 ELGGSFFEPTILADVTPAMKVAREETFGPVAPLFRFETEEEAVRMANATEFGLAAYFYSR 433

Query: 422 DLARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLG 481
           D+ RV+RVAE LEYG+VGIN G+IS EVAPFGG+K SG+GREGSKYGIEDYLEIKYLC+G
Sbjct: 434 DIGRVWRVAEALEYGIVGINEGIISTEVAPFGGMKESGIGREGSKYGIEDYLEIKYLCMG 493

Query: 482 GI 483
           GI
Sbjct: 494 GI 495


Lambda     K      H
   0.317    0.135    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: 767
Number of extensions: 14
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: 483
Length of database: 497
Length adjustment: 34
Effective length of query: 449
Effective length of database: 463
Effective search space:   207887
Effective search space used:   207887
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