GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Azospirillum brasilense Sp245

Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate AZOBR_RS31550 AZOBR_RS31550 acyl-CoA dehydrogenase

Query= reanno::pseudo3_N2E3:AO353_25680
         (375 letters)



>FitnessBrowser__azobra:AZOBR_RS31550
          Length = 392

 Score =  270 bits (690), Expect = 5e-77
 Identities = 154/376 (40%), Positives = 235/376 (62%), Gaps = 8/376 (2%)

Query: 5   DEQLQ-ISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTG 63
           DEQ + I D+  +F    ++P A + + +  +P E +  M ELG FG  +PE++GG    
Sbjct: 14  DEQDRLILDSVDRFLDRHVRPVALKLEHDDTYPDEIVERMKELGLFGATIPEEYGGLGLR 73

Query: 64  YLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFAL 123
              YA  +E I++   + S I++ H  +  + + K G ++QK  FL   A+G + G  AL
Sbjct: 74  PSTYAKMIERISSVWMSLSGIINSHLIMAFI-VTKTGTEEQKAAFLPRFATGELRGGLAL 132

Query: 124 TEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKR--GISA 181
           TEP  G+D  +++T A+ +GD YV+NG K +IT+G       +   TDP+A  R  G++ 
Sbjct: 133 TEPDCGTDLQAIRTVAKRDGDDYVINGSKTWITNGIQGSCFALLVKTDPTAQPRHKGMTM 192

Query: 182 FIVPTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRL--GEEGEGYKIALANLEG 239
           F+     PG+KV+R  +KLG    D+ +++FED +VP A+RL  G EG G   A++ LE 
Sbjct: 193 FLAEK-GPGFKVSRKLEKLGYKGIDSAELVFEDYRVP-ADRLIGGVEGRGMACAISGLEL 250

Query: 240 GRVGIASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHY 299
           GRV +AS+ VG+A+AA + +  Y+++R++FGKPI EHQAVA +LADMAT+++ AR +V  
Sbjct: 251 GRVNVASRGVGVAQAALDESVKYSQQRKTFGKPIHEHQAVAMKLADMATRVSAARLLVQQ 310

Query: 300 AAALRDSGKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQI 359
           AA   D G+    EA MAKLFASE A +    A++  GGYGY  +F +ER+YRD  +  I
Sbjct: 311 AAKALDRGERCDYEAGMAKLFASEAAVENSLDAMRIHGGYGYSKEFVVERLYRDAPLLCI 370

Query: 360 YEGTSDIQRMVISRNL 375
            EGT++IQR++I++ L
Sbjct: 371 GEGTNEIQRIIIAKRL 386


Lambda     K      H
   0.319    0.134    0.389 

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: 320
Number of extensions: 10
Number of successful extensions: 4
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: 375
Length of database: 392
Length adjustment: 30
Effective length of query: 345
Effective length of database: 362
Effective search space:   124890
Effective search space used:   124890
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 (21.8 bits)
S2: 50 (23.9 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