GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__azobra:AZOBR_RS09720 AZOBR_RS09720
           succinate-semialdehyde dehdyrogenase
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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