GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Azospirillum brasilense Sp245

Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate AZOBR_RS29750 AZOBR_RS29750 aldehyde dehydrogenase

Query= reanno::WCS417:GFF827
         (481 letters)



>FitnessBrowser__azobra:AZOBR_RS29750
          Length = 484

 Score =  525 bits (1351), Expect = e-153
 Identities = 258/479 (53%), Positives = 344/479 (71%), Gaps = 6/479 (1%)

Query: 4   AQRFDNYINGQWVAGADYCVNLNPSELSDVIGEYAKADVTQVNAAIDAARAAFPAWSTSG 63
           + R  N+I G W  G +    +NPS L ++ G Y+ A    V  A+ AARAA P W  + 
Sbjct: 5   SDRITNFIAGSWRPGRERLDIVNPSNLDELAGSYSLAGADDVAEAVAAARAAQPQWRAAT 64

Query: 64  IQARHDALDKVGSEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLRLSG 123
           ++ R   LD +   +  R++EL  + A E GKT+P+A+GE+TRA ++ +FFA E LR  G
Sbjct: 65  VEQRSLVLDAISRALFDRKDELARIAATEGGKTIPDALGEITRAAHLARFFAAEALRAPG 124

Query: 124 DYVPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELVPGC 183
           + + SVRPGV V+VTRE +GV+GL+TPWNFP+A P WKIAPALA+GN V+ KP+E  PG 
Sbjct: 125 ETLGSVRPGVEVDVTREPVGVIGLVTPWNFPVATPMWKIAPALAFGNAVIWKPSEKTPGI 184

Query: 184 AWALAEIISRA----GFPAGVFNLVMGSGRVVGDVLVNSPKVDGISFTGSVGVGRQIAVS 239
           + A+  +I+ A    G PA +FNLV+G+G  +G  +V++  VD +SFTGSV  GR+IAV 
Sbjct: 185 SIAVTRLIAEALEAHGMPAALFNLVIGAGPNIGAAVVDA--VDAVSFTGSVNTGRRIAVR 242

Query: 240 CVSRQAKVQLEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRLIVTAGIHDQ 299
           C  R  +VQLE+GG+NP ++L DAD ++A E+ V SA++  GQRCTA+ R IV   IHD 
Sbjct: 243 CAERMIRVQLELGGQNPLVVLGDADPERAAEIGVNSAYFHAGQRCTATGRFIVEDSIHDA 302

Query: 300 FVAAMAERMKSIKVGHALKSGTDIGPVVSQAQLDQDLKYIDIGQSEGARLVSGGGLVTCD 359
           FVAAM ERM +++VGHAL   T IGPV+ + QL ++L YID G  EGA+L SGGG +   
Sbjct: 303 FVAAMTERMAALRVGHALLPETQIGPVIDEFQLTKNLHYIDTGLKEGAQLASGGGRLDRP 362

Query: 360 TEGYYLAPTLFADSEAAMRISREEIFGPVANVVRVADYEAALAMANDTEFGLSAGIATTS 419
           T G++LAPTLF ++  AM I+REE+FGPVA+V+RV DYE AL +ANDT++GLS+GI T S
Sbjct: 363 TRGWFLAPTLFTETSNAMTINREEVFGPVASVIRVKDYEEALHVANDTDYGLSSGIITNS 422

Query: 420 LKYANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSY 478
           +K+A HF+ + QAGM M+NLPTAGVDYHVPFGGRK SSYG REQGR A EFYT++KT+Y
Sbjct: 423 MKHARHFQANIQAGMTMLNLPTAGVDYHVPFGGRKMSSYGPREQGRSAIEFYTIIKTAY 481


Lambda     K      H
   0.318    0.134    0.390 

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: 575
Number of extensions: 19
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: 481
Length of database: 484
Length adjustment: 34
Effective length of query: 447
Effective length of database: 450
Effective search space:   201150
Effective search space used:   201150
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