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.

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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