Alignments for a candidate for davD in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for davD in Klebsiella michiganensis M5al

Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate BWI76_RS05620 BWI76_RS05620 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::Q88RC0
         (480 letters)



>FitnessBrowser__Koxy:BWI76_RS05620
          Length = 482

 Score =  787 bits (2033), Expect = 0.0
 Identities = 392/482 (81%), Positives = 431/482 (89%), Gaps = 2/482 (0%)

Query: 1   MQLKDAQLFRQQAYINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKA 60
           MQL D  LFRQQA ING W DA   +T+ VTNPA G+ +G VPKMG  ETR AI+AA +A
Sbjct: 1   MQLNDPTLFRQQAMINGRWRDASGKETLAVTNPANGQPLGNVPKMGAGETREAIDAAARA 60

Query: 61  LPAWRALTAKERSAKLRRWFELMIENQDDLARLMTTEQGKPLAEAKGEIAYAASFIEWFA 120
           LPAWRALTAKERS+ LRRWFELM+E+QDDLARLMT EQGKPLAEAKGEI+YAASFIEWFA
Sbjct: 61  LPAWRALTAKERSSILRRWFELMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFA 120

Query: 121 EEAKRIYGDTIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLK 180
           EE KRIYGDTIPGHQ DKRL+VIKQPIGVTAAITPWNFP+AMITRKAGPALAAGCTMVLK
Sbjct: 121 EEGKRIYGDTIPGHQADKRLLVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLK 180

Query: 181 PASQTPYSALALVELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQ 240
           PASQTP+SALAL ELA+RAGIP GV +VVTGSA EVGGELTGN LVRKLSFTGSTEIGRQ
Sbjct: 181 PASQTPFSALALAELANRAGIPEGVFNVVTGSASEVGGELTGNPLVRKLSFTGSTEIGRQ 240

Query: 241 LMEECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDG 300
           LME+CAKDIKKVSLELGGNAPFIVFDDADLDKAVEGA+ SK+RN GQTCVCANR+YVQD 
Sbjct: 241 LMEQCAKDIKKVSLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQDS 300

Query: 301 VYDAFAEKLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKL 360
           VYD FAEKL  AV+KL+IG+GL+   T GPLID KA+AKVQEHI DA+ KGA+V++GGK 
Sbjct: 301 VYDRFAEKLQQAVSKLQIGDGLQPNVTIGPLIDEKAIAKVQEHIADALGKGARVVTGGKA 360

Query: 361 IE--GNFFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYA 418
            E  GNFF+PTILVDVP  A VAKEETFGPLAPLFRFKDEA+VIA +NDTEFGLA+YFYA
Sbjct: 361 HELGGNFFQPTILVDVPGDAKVAKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFYA 420

Query: 419 RDMSRVFRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCI 478
           RD+ RVFRV EALEYG++GINTGLIS EVAPFGG+K+SGLGREGSKYGIEDYLEIKY+CI
Sbjct: 421 RDLGRVFRVGEALEYGIIGINTGLISTEVAPFGGVKSSGLGREGSKYGIEDYLEIKYMCI 480

Query: 479 SV 480
            +
Sbjct: 481 GI 482


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: 807
Number of extensions: 22
Number of successful extensions: 2
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: 482
Length adjustment: 34
Effective length of query: 446
Effective length of database: 448
Effective search space:   199808
Effective search space used:   199808
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: 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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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 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