GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Paraburkholderia bryophila 376MFSha3.1

Align 2-methyl-branched-chain-enoyl-CoA reductase (EC 1.3.8.5) (characterized)
to candidate H281DRAFT_02091 H281DRAFT_02091 hypothetical protein

Query= reanno::acidovorax_3H11:Ac3H11_2996
         (376 letters)



>FitnessBrowser__Burk376:H281DRAFT_02091
          Length = 378

 Score =  574 bits (1480), Expect = e-168
 Identities = 284/377 (75%), Positives = 327/377 (86%), Gaps = 2/377 (0%)

Query: 1   MLLTQDQEMIRDAVRDFAQTELWPHAARWDKEHHFPKDAHQGLAALGAYGICVPEEFGGA 60
           M+L QD  M+RDA+R F +  + P+AA WD+E  FPKD H+ LA LGAYG+ VPE +GGA
Sbjct: 1   MVLDQDHLMVRDALRTFVREAVTPYAATWDRERTFPKDVHRQLAELGAYGVLVPETYGGA 60

Query: 61  NLDYLTLALVLEEIAAGDGGTSTAISVTNCPVNAILMRYGNAQQKRDWLTPLARGEMLGA 120
            +D L LAL+LEEIAAGDGGTSTAISV NCPV +IL+ YGN  QKR+WLTPLARGEMLGA
Sbjct: 61  GMDALALALILEEIAAGDGGTSTAISVNNCPVCSILLTYGNDAQKREWLTPLARGEMLGA 120

Query: 121 FCLTEPHVGSDASALRTTAV--KQGDEYVINGVKQFITSGKNGQVAIVIAVTDKGAGKKG 178
           FCLTEP  GSDASALRTTA   K GD YV+NGVKQFITSGKNG VAIV+AVTDK AGK+G
Sbjct: 121 FCLTEPQAGSDASALRTTATRDKDGDAYVLNGVKQFITSGKNGDVAIVMAVTDKAAGKRG 180

Query: 179 MSAFLVPTNNPGYVVARLEDKLGQHSSDTAQINFDNCRIPAENLIGAEGEGYKIALGALE 238
           +SAF+VPT++ GYVVAR+EDKLGQHSSDTAQI F++CR+PA NLIGAEGEGY+IAL  LE
Sbjct: 181 ISAFIVPTDSKGYVVARVEDKLGQHSSDTAQIIFEDCRVPAANLIGAEGEGYRIALSGLE 240

Query: 239 GGRIGIAAQSVGMARSAFDAALAYSKERESFGTAIFNHQAVGFRLADCATQIEAARQLIW 298
           GGRIGIAAQSVGMAR+A++AAL Y+KERESFG  +F+HQAV FRLAD ATQ+EAARQLIW
Sbjct: 241 GGRIGIAAQSVGMARAAYEAALTYAKERESFGQPLFSHQAVQFRLADMATQLEAARQLIW 300

Query: 299 HAAALRDAGKPCLKEAAMAKLFASEMAERVCSAAIQTLGGYGVVNDFPVERIYRDVRVCQ 358
           HAA+L+DAG+PCL EAAMAKLFASE AER+CSAA+Q  GGYG ++DFPVERIYRDVRVCQ
Sbjct: 301 HAASLKDAGQPCLTEAAMAKLFASEAAERICSAALQIHGGYGYLSDFPVERIYRDVRVCQ 360

Query: 359 IYEGTSDVQKIIIQRAL 375
           IYEGTSD+QKI+I R L
Sbjct: 361 IYEGTSDIQKILIARGL 377


Lambda     K      H
   0.319    0.134    0.396 

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: 527
Number of extensions: 20
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: 376
Length of database: 378
Length adjustment: 30
Effective length of query: 346
Effective length of database: 348
Effective search space:   120408
Effective search space used:   120408
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: 50 (23.9 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:

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