GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Dyella japonica UNC79MFTsu3.2

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate N515DRAFT_0379 N515DRAFT_0379 Acyl-CoA reductase

Query= metacyc::MONOMER-15108
         (486 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0379
          Length = 476

 Score =  213 bits (542), Expect = 1e-59
 Identities = 148/446 (33%), Positives = 231/446 (51%), Gaps = 20/446 (4%)

Query: 42  VAEGGAAEIDLAVQAAKKALNGPWKKMTANERIAVLRKVGDLILERKEELSVLESLDTGK 101
           VA   A   + A+ AA KA   P ++    ER AVL+       ER++EL+    ++ GK
Sbjct: 35  VAVPDAKATEQAIAAAVKAAE-PMRQFKPWERQAVLQHCVQRFTERRDELAYALCVEAGK 93

Query: 102 PTWLSGSIDIPRAAYNFHFFSDYI-----RTITNEATQMDDVALNYAIRRPVGVIGLINP 156
           P   S   ++ R    F   ++        TI  E  +  +    Y  R P+G +  I P
Sbjct: 94  PIKDSAG-EVTRLIETFGIAAEEAVRTNGETINLEIAKRLNGYHGYTRRVPLGPVSFITP 152

Query: 157 WNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATVLAEICRDAGVPDGVVNLVHGFGPN 216
           +N PL L+  K+APA+AAG   V+KPAE TP+ A ++ E+  +  +P G  ++++  G +
Sbjct: 153 FNFPLNLVAHKVAPAIAAGCPFVLKPAERTPIGALIIGEVLAETDLPKGAFSILNLDGKH 212

Query: 217 SAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLKRLSYELGGKNPNVIFADS--NLDE 274
           ++   L E P    +SFTG +  G  +   A    K+++ ELGG    ++ AD    LD 
Sbjct: 213 AS--PLVEDPRFKLLSFTG-SQIGWDLKTRAGH--KKVTLELGGNAACIVDADQLPRLDH 267

Query: 275 VIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFVAKTKELVVGDPFDAKTKVGALI 334
           VIE  +  +F   G+ C+   RIY     Y+   ++ VA  K L  GDP   +T +G +I
Sbjct: 268 VIERLVFGAFYQSGQSCISVQRIYAHESLYDELKKRLVAAVKGLKAGDPKKKETFLGPMI 327

Query: 335 SDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKGYFLEPTIITGLTRDCRVVKEEIFGP 394
            +   ER+ G+I+ A + GG +L GGKR     KG  LE T++  +  D +V ++E+FGP
Sbjct: 328 DEAAAERLHGWIEEARKGGGKVLCGGKR-----KGPMLEATLMENVRGDAKVNRQEVFGP 382

Query: 395 VVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAHRVAGQIEAGIVWVN-TWFLRDLR 453
              + PF + +E +   ND+ YGL A ++T+ L  A R   ++E G V VN     R   
Sbjct: 383 FALLAPFKSLDEAIAMTNDSDYGLQAGIFTDSLANAMRAWNELEQGGVIVNDVPSFRVDN 442

Query: 454 TPFGGMKQSGIGREGGLHSFEFYSEL 479
            P+GG+K SG GREG  ++ E  +E+
Sbjct: 443 MPYGGVKLSGAGREGVRYAIEDMTEI 468


Lambda     K      H
   0.318    0.136    0.404 

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: 542
Number of extensions: 31
Number of successful extensions: 5
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: 486
Length of database: 476
Length adjustment: 34
Effective length of query: 452
Effective length of database: 442
Effective search space:   199784
Effective search space used:   199784
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 (21.7 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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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