Alignments for a candidate for adh in Klebsiella variicola At-22

GapMind for catabolism of small carbon sources

Alignments for a candidate for adh in Klebsiella variicola At-22

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_012968349.1 KVAR_RS14215 succinylglutamate-semialdehyde dehydrogenase

Query= BRENDA::P76217
         (492 letters)



>NCBI__GCF_000025465.1:WP_012968349.1
          Length = 488

 Score =  633 bits (1632), Expect = 0.0
 Identities = 309/483 (63%), Positives = 374/483 (77%), Gaps = 1/483 (0%)

Query: 4   WINGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAERHA 63
           +I G W  G GA+  K  P    +LWQ   A A  V+ AC AARAAF  W+    AER A
Sbjct: 7   FIAGQWQAGSGATMSKLAPEDQSLLWQAASAGADDVQAACAAARAAFYPWSHRPLAERIA 66

Query: 64  VVERFAALLESNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQRSEM 123
           VVERFAALLE++K  L  +I+RET KP WE  TEV AMI K AISI+AYH RTG   S +
Sbjct: 67  VVERFAALLETHKEALATLISRETSKPLWETRTEVQAMIGKAAISIEAYHQRTGFHESTL 126

Query: 124 PDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAVMRL 183
           PDG A LRH+PHGV+AVFGPYNFPGHLPNGHI+PAL+AGNTI+FKPSELTP + E  ++L
Sbjct: 127 PDGKAQLRHKPHGVMAVFGPYNFPGHLPNGHIIPALIAGNTIVFKPSELTPATAEMTVQL 186

Query: 184 WQQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKILALE 243
           WQQAG+P GV+NL+QGG+ TGQAL    D+DG+LFTGSA  G+  HR   GQPEK+LALE
Sbjct: 187 WQQAGVPDGVINLLQGGKTTGQALLENRDIDGVLFTGSAAAGFHFHRYFGGQPEKMLALE 246

Query: 244 MGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVAVSQ 303
           MGGNN LI+ +VAD+DAA+H+ IQSAF++AGQRCTCARRL++  G QGDA L RLVA S 
Sbjct: 247 MGGNNALIVADVADVDAALHVIIQSAFISAGQRCTCARRLIVPRGEQGDALLQRLVAASA 306

Query: 304 RLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSLLTPGII 363
           ++  G WDD+P PF+GG+IS  AAQ ++ A Q+LE +GG+ LL  R     +++LTPGI+
Sbjct: 307 QIRAGKWDDQPAPFMGGVISLDAAQNMLAAQQKLEGLGGKVLLRMRQPDPRSTVLTPGIV 366

Query: 364 EMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLLEAR 423
           ++TG+  VPDEE FGPLL V RYD F EAIR+AN TR+GL+ GL+S +  +FDQL  EAR
Sbjct: 367 DVTGIE-VPDEEYFGPLLTVIRYDDFPEAIRLANQTRYGLAVGLISSDAAQFDQLADEAR 425

Query: 424 AGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAADYCAWPMASLESDSLTLPATLNPG 483
           AGIVNWNKPLTGA+S APFGG+GASGNHR +AWYAADYCAWPMASL SD+LTLPAT++PG
Sbjct: 426 AGIVNWNKPLTGASSKAPFGGVGASGNHRAAAWYAADYCAWPMASLVSDTLTLPATVSPG 485

Query: 484 LDF 486
           L F
Sbjct: 486 LPF 488


Lambda     K      H
   0.318    0.134    0.412 

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: 796
Number of extensions: 27
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: 492
Length of database: 488
Length adjustment: 34
Effective length of query: 458
Effective length of database: 454
Effective search space:   207932
Effective search space used:   207932
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 (21.7 bits)
S2: 52 (24.6 bits)

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

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Protein sequences (fasta format)
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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