Alignments for a candidate for gabD in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabD in Klebsiella michiganensis M5al

Align aldehyde dehydrogenase-like protein yneI (characterized)
to candidate BWI76_RS15205 BWI76_RS15205 succinate-semialdehyde dehydrogenase

Query= CharProtDB::CH_024181
         (462 letters)



>FitnessBrowser__Koxy:BWI76_RS15205
          Length = 461

 Score =  725 bits (1871), Expect = 0.0
 Identities = 350/456 (76%), Positives = 396/456 (86%)

Query: 6   ATHAISINPATGEQLSVLPWAGADDIENALQLAAAGFRDWRETNIDYRAEKLRDIGKALR 65
           ATHA+S+NP TGE LS LPWA    +++A+ LA  G+R WR+ ++  RA  LR++G A+R
Sbjct: 5   ATHAVSVNPTTGETLSSLPWASEQQVDSAIALAEQGYRQWRKVSVAQRATTLRNVGAAMR 64

Query: 66  ARSEEMAQMITREMGKPINQARAEVAKSANLCDWYAEHGPAMLKAEPTLVENQQAVIEYR 125
           ARSE +AQMI+ EMGKPI QAR EVAKSANLCDWYAEHGPAML  E TLVE+ +AVIEYR
Sbjct: 65  ARSEALAQMISLEMGKPIAQARGEVAKSANLCDWYAEHGPAMLNTEATLVEDNKAVIEYR 124

Query: 126 PLGTILAIMPWNFPLWQVMRGAVPIILAGNGYLLKHAPNVMGCAQLIAQVFKDAGIPQGV 185
           P+G ILAIMPWNFP+WQV+RGAVPI+LAGN YLLKHAPNV+G A +I ++F  AG+P+GV
Sbjct: 125 PMGAILAIMPWNFPVWQVLRGAVPILLAGNSYLLKHAPNVLGSAAMIGEIFAAAGVPEGV 184

Query: 186 YGWLNADNDGVSQMIKDSRIAAVTVTGSVRAGAAIGAQAGAALKKCVLELGGSDPFIVLN 245
           +GW+NA NDGVSQMI D RIAAVTVTGSVRAG AIGAQAGAALKKCVLELGGSDPFIVLN
Sbjct: 185 FGWVNATNDGVSQMINDPRIAAVTVTGSVRAGKAIGAQAGAALKKCVLELGGSDPFIVLN 244

Query: 246 DADLELAVKAAVAGRYQNTGQVCAAAKRFIIEEGIASAFTERFVAAAAALKMGDPRDEEN 305
           DADL+ AVKAAV GRYQNTGQVCAAAKRFI+E GIA AFT++FVAA AALKMGDPRDE+N
Sbjct: 245 DADLDEAVKAAVIGRYQNTGQVCAAAKRFIVEAGIAEAFTQKFVAAVAALKMGDPRDEQN 304

Query: 306 ALGPMARFDLRDELHHQVEKTLAQGARLLLGGEKMAGAGNYYPPTVLANVTPEMTAFREE 365
            +GPMARFDLRDELH QV  TL +GA LLLG EK+ GAGNYY PTVL NVT EMT FREE
Sbjct: 305 YIGPMARFDLRDELHEQVRATLKEGATLLLGAEKIEGAGNYYAPTVLGNVTAEMTGFREE 364

Query: 366 MFGPVAAITIAKDAEHALELANDSEFGLSATIFTTDETQARQMAARLECGGVFINGYCAS 425
           +FGPVA IT A+DA+HAL LAN+SEFGLSAT++TT ETQAR+ A  LECGGVFINGYCAS
Sbjct: 365 LFGPVATITEARDADHALALANESEFGLSATVYTTSETQARRFADELECGGVFINGYCAS 424

Query: 426 DARVAFGGVKKSGFGRELSHFGLHEFCNIQTVWKDR 461
           DARVAFGGVKKSGFGRELSHFGLHEFCN+QTVW+DR
Sbjct: 425 DARVAFGGVKKSGFGRELSHFGLHEFCNVQTVWRDR 460


Lambda     K      H
   0.319    0.134    0.397 

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: 11
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: 462
Length of database: 461
Length adjustment: 33
Effective length of query: 429
Effective length of database: 428
Effective search space:   183612
Effective search space used:   183612
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
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