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.- (characterized)
to candidate H281DRAFT_03540 H281DRAFT_03540 succinate semialdehyde dehydrogenase (EC 1.2.1.16)

Query= SwissProt::Q9I6M5
         (483 letters)



>FitnessBrowser__Burk376:H281DRAFT_03540
          Length = 479

 Score =  621 bits (1602), Expect = 0.0
 Identities = 299/477 (62%), Positives = 373/477 (78%), Gaps = 2/477 (0%)

Query: 7   KLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALPAWRA 66
           +  R   Y+ G W +     T  V NPATGE+I  V K GA E  +AI AA++A PAWR+
Sbjct: 3   EFLRTGHYIGGEWYEG--ASTYPVLNPATGEVIAQVAKGGAVEATQAIAAAERAFPAWRS 60

Query: 67  LTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFGEEAKRI 126
           LTAKER+ +++RW +LM+E++D LA L+T EQGKPLAEA+GE+ YAASF EWF EEAKR 
Sbjct: 61  LTAKERSARVKRWGELMLEHRDALAALLTREQGKPLAEARGEVGYAASFFEWFAEEAKRA 120

Query: 127 YGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTP 186
           YGD IP   P+ +IIV ++P+GV AAITPWNFP AMITRKAGPALAAGCTMVLKP+ +TP
Sbjct: 121 YGDVIPSPNPNAKIIVTREPVGVVAAITPWNFPLAMITRKAGPALAAGCTMVLKPSEETP 180

Query: 187 YSALALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQLMAECA 246
            SALALA LAE+AGIP GVF+VV+G A  +GG LT + +VRKL+FTGST +G+ L  + A
Sbjct: 181 LSALALAVLAEKAGIPPGVFNVVSGDAVAIGGALTESDVVRKLSFTGSTRVGKLLAKQSA 240

Query: 247 QDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVYDAFV 306
             +KK+SLELGGNAPFIVFDDADLDAAV+GA+ SK+RN GQTCVC NR YVQDG+YDAF 
Sbjct: 241 DTLKKLSLELGGNAPFIVFDDADLDAAVQGAMASKFRNTGQTCVCVNRFYVQDGIYDAFT 300

Query: 307 DKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPHALGGT 366
             L  A  K+ +GN L+  V  GPLI+  A+ KVE H+ADA+ KGAKV++G KPHALGGT
Sbjct: 301 LALAQAARKMRVGNALQGDVEQGPLINQAALTKVEAHVADALQKGAKVLTGAKPHALGGT 360

Query: 367 FFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARDLARV 426
           F+EPT+LVD   + L++++ETFGP+A  FRFK E E +A +N T FGL++YFY RDLAR 
Sbjct: 361 FYEPTVLVDASSSMLIAQEETFGPVAACFRFKTEDEAVAAANATPFGLSAYFYTRDLARA 420

Query: 427 FRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLGGI 483
           +RV E LE GMVGIN G++S EVAPFGG+K SGLGREGSKYG+++Y E+KY+ +GG+
Sbjct: 421 WRVGEALESGMVGINEGILSTEVAPFGGVKQSGLGREGSKYGLDEYTELKYMMMGGL 477


Lambda     K      H
   0.317    0.135    0.391 

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: 655
Number of extensions: 12
Number of successful extensions: 1
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: 483
Length of database: 479
Length adjustment: 34
Effective length of query: 449
Effective length of database: 445
Effective search space:   199805
Effective search space used:   199805
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: 51 (24.3 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:

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