Alignments for a candidate for dopDH in Azospirillum brasilense Sp245

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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources