GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Azospirillum brasilense Sp245

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate AZOBR_RS19635 AZOBR_RS19635 succinate-semialdehyde dehydrogenase

Query= BRENDA::P51650
         (523 letters)



>FitnessBrowser__azobra:AZOBR_RS19635
          Length = 485

 Score =  570 bits (1468), Expect = e-167
 Identities = 276/478 (57%), Positives = 370/478 (77%), Gaps = 5/478 (1%)

Query: 46  LLRGDSFVGGRWLP--TPATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEI 103
           LLR  ++V G W    +  TF V +PA+G +L  VAD G  E R A+ AA  A  +W+  
Sbjct: 8   LLRTQAYVNGVWRDAFSGKTFAVTNPATGEELAQVADVGAEETRQAINAADAALPAWRAK 67

Query: 104 SVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVY 163
           + KER+++LR+W++L++  +++LA ++T E GKPL EA+GE+ Y A F+EWF+EE +RVY
Sbjct: 68  TAKERAAILRRWFELIMAAQEDLAVLMTLEQGKPLAEARGEVAYGASFIEWFAEEGKRVY 127

Query: 164 GDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPY 223
           GD+I + A +KR +VLK+P+GV + ITPWNFP+AMITRKVG ALAAGCT+VVKPAEDTP 
Sbjct: 128 GDVIPSFAGNKRIVVLKEPIGVVAAITPWNFPNAMITRKVGPALAAGCTIVVKPAEDTPL 187

Query: 224 SALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHH 283
           SALALA+LA +AG+P GV+N++  S   A  +G  L   P+V K+SFTGST  GKIL+  
Sbjct: 188 SALALAELAERAGVPAGVFNIVTGSDPVA--IGGELTASPIVRKLSFTGSTEVGKILMRQ 245

Query: 284 AANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDS 343
           +A++VK+VS+ELGG APFIVFD A++D+AV GA+ASK+RN+GQTCVC+NR LVQ G++D+
Sbjct: 246 SADTVKKVSLELGGNAPFIVFDDADLDEAVKGALASKYRNSGQTCVCANRLLVQAGVYDA 305

Query: 344 FVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQS 403
           F  K AEA+K+ +RVGNG E G TQGP+IN +AVEKVE+ + DA+AKGA V  GGKRH  
Sbjct: 306 FAAKLAEAVKQ-IRVGNGMEAGVTQGPMINGQAVEKVEELMGDALAKGAKVALGGKRHGL 364

Query: 404 GGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDP 463
           GG FFEPT+L+ VT +M    EE FGPVAP+ KF+ E +A+ +AN  + GLA YFYS+D 
Sbjct: 365 GGTFFEPTILTGVTTEMRVAREEIFGPVAPLFKFETEADAIRMANDTEFGLAAYFYSRDI 424

Query: 464 AQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYG 521
            ++WRVAEQLE GMVG+NEG++S+   PFGG+KQSG+GREGSKYG++++LE+KY+C G
Sbjct: 425 GRVWRVAEQLEYGMVGINEGILSTEVAPFGGIKQSGIGREGSKYGVEDFLEIKYLCVG 482


Lambda     K      H
   0.318    0.135    0.400 

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: 688
Number of extensions: 26
Number of successful extensions: 3
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: 523
Length of database: 485
Length adjustment: 34
Effective length of query: 489
Effective length of database: 451
Effective search space:   220539
Effective search space used:   220539
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