GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_0379 N515DRAFT_0379 Acyl-CoA
           reductase
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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