GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Methylocystis bryophila S285

Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate WP_085772038.1 B1812_RS13395 aldehyde dehydrogenase family protein

Query= SwissProt::P42236
         (488 letters)



>NCBI__GCF_002117405.1:WP_085772038.1
          Length = 506

 Score =  274 bits (701), Expect = 5e-78
 Identities = 180/485 (37%), Positives = 253/485 (52%), Gaps = 15/485 (3%)

Query: 10  YLNFINGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEAKTAWRKLTG 69
           Y NFI G+WV    G+     +P   + I   V    A DVE A+ AA++AK AW K   
Sbjct: 19  YDNFIGGQWVAPLGGEYFDNISPITGHPIC-QVARGRAADVELALDAAHKAKDAWGKTPA 77

Query: 70  AERGQYLYKTADIMEQRLEEIAACATREMGKTLPEAKG-ETARGIAILRYYAGEGMRKTG 128
           AER   L K A  ++  L  +A   T + GK + E    +    I   RY+AG  +R   
Sbjct: 78  AERANMLNKIAQRLDDNLSALALVETIDNGKPIRETTAADIPLAIDHFRYFAG-CLRAQE 136

Query: 129 DVIPSTDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVIKPATETAVT 188
             +   D D + +    PLGVVG I PWNFP+ +  WK++PAL  GN VV+KPA +T ++
Sbjct: 137 GSLSEIDHDTVAYHFHEPLGVVGQIIPWNFPILMAAWKLSPALAAGNCVVLKPAEQTPMS 196

Query: 189 CAKIIACFEEAGLPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGKIIGQAALAR 248
              +     +  LP GV+N+V G G   G+ LA +  +  + FTG    G++I Q A   
Sbjct: 197 ILAVAELIADL-LPPGVLNIVNGFGVEAGKPLASNKRIAKIAFTGETTTGRLIMQYAAEN 255

Query: 249 GAKYQLEMGGKNP------VIVADDADLEAAAEAVITGAFRSTGQKCTATSRVIVQSGIY 302
                LE+GGK+P      V+  DDA L+ A E   + A    G+ CT  SR +VQ  IY
Sbjct: 256 LIPVTLELGGKSPNIFFADVMAEDDAFLDKALEGFASFALNQ-GEVCTCPSRALVQRSIY 314

Query: 303 ERFKEKLLQRTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGGEK-L 361
           ++F EK L R   I  G  L     +G  AS +QL+  LSY++ G++EGA +LIGGE+ +
Sbjct: 315 DKFMEKALARVAKIRQGHPLDPATMIGAQASNDQLEKILSYVDIGRKEGAKVLIGGERSV 374

Query: 362 ENGKYQNGYYVQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGLSAS 421
             G+ + GYY+QP   +   + M + QEEIFGPV+++   ++ EEAL IAND  +GL A 
Sbjct: 375 LEGELKEGYYMQPTALEG-HNRMRVFQEEIFGPVVSVTTFETEEEALQIANDTLYGLGAG 433

Query: 422 IFTENIGRMLSFIDEIDAGLVRINAESAGVELQAPFGGMKQSSSHSREQGEAAKDFFTAI 481
           ++T +  R       I AG V  N   A     A FGG KQS    RE  +   D +   
Sbjct: 434 LWTRDGSRAYRCGRAIRAGRVWTNCYHA-YPAHAAFGGYKQSGI-GRENHKMMLDHYQQT 491

Query: 482 KTVFV 486
           K + V
Sbjct: 492 KNLLV 496


Lambda     K      H
   0.315    0.132    0.374 

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: 529
Number of extensions: 25
Number of successful extensions: 7
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: 488
Length of database: 506
Length adjustment: 34
Effective length of query: 454
Effective length of database: 472
Effective search space:   214288
Effective search space used:   214288
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 (21.5 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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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