GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Azospirillum brasilense Sp245

Align succinate-semialdehyde dehydrogenase [NAD(P)+]; EC 1.2.1.16 (characterized)
to candidate AZOBR_RS32475 AZOBR_RS32475 aldehyde Dehydrogenase

Query= CharProtDB::CH_007085
         (453 letters)



>FitnessBrowser__azobra:AZOBR_RS32475
          Length = 475

 Score =  296 bits (758), Expect = 1e-84
 Identities = 172/458 (37%), Positives = 267/458 (58%), Gaps = 9/458 (1%)

Query: 2   SNEVSIKELIEKAKVAQKKLEAYSQEQVDVLVKALGKVVYD--NAEMFAKEAVEETEMGV 59
           +++ +I  L+ +A+ AQ+     +QE+VD  V AL   +Y+   A   A+ AV +T +G 
Sbjct: 13  ADQEAIAALVARARTAQRAFADATQERVDDAVAALAWAIYEPGRARALAELAVADTGLGN 72

Query: 60  YEDKVAKCHLKSGAIWNHIKDKKTVGIIKEEPERALVYVAKPKGVVAATTPITNPVVTPM 119
             DK+ K   K+      +   +TVG+I+E+  + +V +AKP GVV A TP TNP  TP+
Sbjct: 73  VADKIVKNQRKTFGTLRDLMRVRTVGVIEEDTAKGIVKIAKPLGVVGAVTPSTNPAATPV 132

Query: 120 CNAMAAIKGRNTIIVAPHPKAKKVSAHTVELMNAELKKLGAPENIIQIVEAP-SREAAKE 178
             AM A+KGRN II+AP P     +  TVELM AEL ++GAPE+++Q++  P ++   + 
Sbjct: 133 NKAMMAVKGRNAIIIAPSPMGSAATGRTVELMRAELARIGAPEDLVQMIPTPITKGLTQA 192

Query: 179 LMESADVVIATGGAGRVKAAYSSGRPAYGVGPGNSQVIVDKGYDYNKAAQDIITGRKYDN 238
           LME+ D+V+ TG    V+ AYSSG PA GVG GN  VIVD+  D  +AA+ I   + +DN
Sbjct: 193 LMEAVDLVVVTGSQDNVRRAYSSGTPAIGVGAGNVPVIVDESADLAEAARKIGASKTFDN 252

Query: 239 GIICSSEQSVIAPAEDYDKVIAAFVENGAFYVEDEETVEKFRSTLFKDGKINSKIIGKSV 298
              CSSE +++     YD  IAA  E GA     EE  E+ +S L+++GK+N K+I K  
Sbjct: 253 STSCSSENALVVLDSVYDATIAALEEAGAHLCTPEER-ERVQSRLWENGKLNRKLIAKDP 311

Query: 299 QIIADLAGVKVPEG--TKVIVLKGKGAGEKDVLCKEKMCPVLVALKYDTFEEAVEIAMAN 356
            I+A+ A    P+    +  +++  G G+      EK+  VL   +   F+ AV+     
Sbjct: 312 AILAE-AFELAPKAREARFFLVEETGVGKAHPFSGEKLSLVLAVYRVPDFDAAVDQVRKI 370

Query: 357 YMYEGAGHTAGIHSDNDENIRYAGTVLPISRLVVNQPATTA-GGSFNNGFNPTTTLGCGS 415
             ++G GH+ GIH+ ++ + +     L + R++VN   T   GG F++G N T ++GCGS
Sbjct: 371 LDHQGRGHSCGIHTRDEAHAKRLADELDVVRVLVNFAHTFGNGGGFDSGLNFTLSMGCGS 430

Query: 416 WGRNSISENLTYEHLINVSRIGYFNKEAKVPSYEEIWG 453
           W +NSISENL+++H +N++ +     E K PS E ++G
Sbjct: 431 WQKNSISENLSWKHFVNITHLVRPIPEDK-PSEEALFG 467


Lambda     K      H
   0.313    0.131    0.368 

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: 568
Number of extensions: 27
Number of successful extensions: 6
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: 453
Length of database: 475
Length adjustment: 33
Effective length of query: 420
Effective length of database: 442
Effective search space:   185640
Effective search space used:   185640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.3 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