Alignments for a candidate for davD in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for davD in Paraburkholderia bryophila 376MFSha3.1

Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate H281DRAFT_06351 H281DRAFT_06351 succinate semialdehyde dehydrogenase (EC 1.2.1.16)

Query= BRENDA::Q88RC0
         (480 letters)



>FitnessBrowser__Burk376:H281DRAFT_06351
          Length = 491

 Score =  541 bits (1395), Expect = e-158
 Identities = 266/477 (55%), Positives = 342/477 (71%), Gaps = 6/477 (1%)

Query: 7   QLFRQQAYINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRA 66
           +L R   +I G+W+ A NG    VTNPATG+ I  V     A+ R A +AA  ALPAWR 
Sbjct: 9   ELIRPLNFIGGKWIAAANGARFPVTNPATGDTIVEVANSSAADARAATDAAASALPAWRG 68

Query: 67  LTAKERSAKLRRWFELMIENQDDLARLMTTEQGKPLAEAKGEIAYAASFIEWFAEEAKRI 126
              +ER+  LRRW  L++EN +DLA+LM+TEQGKPLAE++GE+AY AS++ WFA+EA RI
Sbjct: 69  KLPRERAEILRRWHALIVENTEDLAKLMSTEQGKPLAESRGEVAYGASYVAWFADEATRI 128

Query: 127 YGDTIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTP 186
           YGD IP  Q  KR+  +K+ IG+ AAITPWNFP AMI RK  PALAAGCT+V KPA  TP
Sbjct: 129 YGDIIPQQQRGKRMSAVKEAIGIVAAITPWNFPLAMIARKIAPALAAGCTVVAKPAEDTP 188

Query: 187 YSALALVELAHRAGIPAGVLSVVTGSAG---EVGGELTGNSLVRKLSFTGSTEIGRQLME 243
            +ALAL  LA  AG+P GVL++++ S     E   +   ++ VRK++FTGST +G+ L  
Sbjct: 189 LTALALAALAQEAGVPDGVLNMLSASRDQGIEAVADWLADARVRKITFTGSTPVGKHLAR 248

Query: 244 ECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYD 303
           E A  +KK+SLELGGNAPFIVFDDADLD AV G + +K+RN GQTCVC NR+YVQ GVY+
Sbjct: 249 ESAATLKKLSLELGGNAPFIVFDDADLDAAVTGLMAAKFRNGGQTCVCPNRVYVQAGVYE 308

Query: 304 AFAEKLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKLIE- 362
            FA+ LA  VA LK+    +     GP+I+ +A+ K+  H+EDAV +GAKVL+GGK +  
Sbjct: 309 RFADLLAKRVAALKVAPATDPSAQIGPMINERAIDKIARHVEDAVKQGAKVLTGGKRLTE 368

Query: 363 --GNFFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARD 420
              N++ PT+L D      V  EETFGP+APLFRF DEAE + ++NDT FGLA+YF+ +D
Sbjct: 369 LGPNYYAPTVLTDANDGMLVCCEETFGPVAPLFRFSDEAEAVRLANDTPFGLAAYFFTQD 428

Query: 421 MSRVFRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLC 477
           + R+ RVA  LE G++GIN G +S+EVAPFGG+K SG GREGSKYG++DYL IKYLC
Sbjct: 429 VRRIDRVATRLEAGVIGINEGAVSSEVAPFGGVKESGYGREGSKYGLDDYLSIKYLC 485


Lambda     K      H
   0.317    0.134    0.384 

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: 646
Number of extensions: 16
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: 480
Length of database: 491
Length adjustment: 34
Effective length of query: 446
Effective length of database: 457
Effective search space:   203822
Effective search space used:   203822
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 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

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

Related tools

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 paper from 2022 on GapMind for carbon sources, or view the source code.

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