GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Azospirillum brasilense Sp245

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate AZOBR_RS29185 AZOBR_RS29185 aldehyde dehydrogenase

Query= curated2:Q2G9T9
         (471 letters)



>FitnessBrowser__azobra:AZOBR_RS29185
          Length = 478

 Score =  208 bits (529), Expect = 4e-58
 Identities = 155/429 (36%), Positives = 206/429 (48%), Gaps = 17/429 (3%)

Query: 14  GAEVWRGKVGDVEEVVARARRAWPAWAAQPLATRIELVRRFANEVRKDADNLATMISRET 73
           G   W   V   EE +  A  A P WAA    TR +++RR  +E+   A+ L  +++RE 
Sbjct: 32  GHYAW-ASVEQAEEALGAAHAALPGWAASNPQTRSDVLRRVGDELNARAEELGALLTREE 90

Query: 74  GKPLWEARTEVDSVVNKVEISIRAYADRTSQRKLDSALQG-----TAALRHKPHGVLAVL 128
           GK L E   EV     +    I  YA     R+   AL G     TA +  +P GV+ ++
Sbjct: 91  GKTLREGIGEV-----RRSAQIFHYAAGEPLRQGGEALPGLRDGTTAMVSREPVGVVVLI 145

Query: 129 GPYNFPAHLPNGHIVPALIAGNAVVFKPSEKTPATGEMLAQCFHRAGIPAAVVQVLIG-G 187
            P+NFP  +P      AL  GN VV KPSE TPA    LA   HRAG+PA    +++G G
Sbjct: 146 TPWNFPMAVPAWKTAYALAFGNTVVLKPSEVTPACAWELADILHRAGLPAGAFNLVVGDG 205

Query: 188 PEEGQALVAHDGIDGVLFTGSAHAGIAINRKLASNPGKIVALEMGGNNPIVVWDTPKIED 247
              G ALV  DG D V FTGS   G AI  +  +   + V LE+GG NP+VV D   +E 
Sbjct: 206 RTLGPALV--DGADAVSFTGSPGVGRAILERSVARMTR-VQLELGGKNPLVVHDDADLEL 262

Query: 248 AATLIVQSAFTSAGQRCTAARRLIIKASMFDEVIDHVKRLADRIIVGAPFDDPAPFMGPV 307
           A  + +Q AF S GQRCTA  R+I+   + D  ++ +      + VG P  D A  MGPV
Sbjct: 263 AVDIALQGAFHSTGQRCTATSRIIVDRRVHDAFVERLVTRIAALRVGDPM-DAATDMGPV 321

Query: 308 IDNRTADGLTESFVYLLSSGGRPIKHMVRLQEDRPFLSPAIIDVTAVADRPD-VELFGPL 366
           +                S G        R+  D  FL P +   T  A R +  E+FGP+
Sbjct: 322 VSEAQLAKDLHCIADARSEGAELAFGGGRMDGDGYFLEPTLFVGTDNAMRINRDEVFGPV 381

Query: 367 LQVVRVDDFDEAIAEANNTRFGLSASLIGGDPQDYNRFWANIRAGVVNWNRPTNGASSAA 426
             V+  D  D AIA AN++   LS+ ++         F    RAG+V  N PT G     
Sbjct: 382 ACVIPADGLDHAIAIANDSDHALSSGIVTRGLASAETFRRRSRAGLVMVNAPTAGIDYHV 441

Query: 427 PFGGVGLSG 435
           PFGG G SG
Sbjct: 442 PFGGRGPSG 450


Lambda     K      H
   0.319    0.135    0.403 

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: 594
Number of extensions: 24
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: 471
Length of database: 478
Length adjustment: 33
Effective length of query: 438
Effective length of database: 445
Effective search space:   194910
Effective search space used:   194910
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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