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

GapMind for catabolism of small carbon sources

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

Align Acyl-coenzyme A synthetase ACSM3, mitochondrial; Acyl-CoA synthetase medium-chain family member 3; Butyrate--CoA ligase 3; Butyryl-coenzyme A synthetase 3; Middle-chain acyl-CoA synthetase 3; Propionate--CoA ligase; Protein SA homolog; EC 6.2.1.2; EC 6.2.1.17 (characterized)
to candidate N515DRAFT_1417 N515DRAFT_1417 long-chain acyl-CoA synthetase

Query= SwissProt::Q3UNX5
         (580 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1417
          Length = 562

 Score =  176 bits (445), Expect = 3e-48
 Identities = 155/544 (28%), Positives = 245/544 (45%), Gaps = 54/544 (9%)

Query: 66  EKAGKRLSNPAFWWIDGNGEELRWSFEELGLLSRKFANILTEACSLQRGDRVMVILPKIP 125
           E   K    PAF      G+EL  S+ ++  LSR+FA  LT    L +GDR+ +++P + 
Sbjct: 33  EAFAKFRDRPAF---HSFGKEL--SYGQIDELSRQFAGYLTGVLKLGKGDRIAIMMPNVL 87

Query: 126 EWWLANVACLRTGTVLIPGTTQLTQKDILYRLQSSKAKCIITDDTLAPAVDAVAAKCENL 185
           ++ +A    LR G V++      T +++ ++L+ + AK I+  D  A  +  V A+ E  
Sbjct: 88  QYPIALFGALRAGLVVVNTNPMYTARELKHQLEDAGAKAIVVLDNFAATLQQVVAETEVE 147

Query: 186 HSKLIVSQHSREGWGN--------LKEMMKYASD-----------------SHTC--VDT 218
           H   IV+    +  G         LK + K   D                 +H    VD 
Sbjct: 148 H---IVTTGIGDLLGLKGTLINFVLKHIKKMVPDYRLPHAVRFRDALAQGAAHPVPKVDL 204

Query: 219 KHDEMMAIYFTSGTTGPPKMIGHTHSSFGLGLSVNGRFWLDLIAS---DVMWNTSDTGWA 275
            HD++  + +T GTTG  K    +H +    +   G  W+   A    +V+         
Sbjct: 205 GHDDLAFLQYTGGTTGVAKGAMLSHGNMVANMLQAGA-WIGTNAKPGEEVIITALPLYHI 263

Query: 276 KSAWSSVFSPWTQGACVFAHYLPRFESTSILQTLSKFPITVFCSAPTAYRMLVQND-MSS 334
            S  ++       G   +    PR +    ++ L K   T      T +  L+     + 
Sbjct: 264 FSLTANGLVFTRLGGLNWLITNPR-DMPGFVKELKKSRFTALTGVNTLFNGLLNTPGFAE 322

Query: 335 YKFNSLKHCVSAGEPINPEVMEQWRKKTGLDIYEGYGQTETV-LICGNFKGMKIKPGSMG 393
             F+ L   +  G  +   V E+W+K TG+ + E YG TET    C N   +K    S+G
Sbjct: 323 VDFSRLHLSLGGGMAVQRAVAERWKKVTGVTLAEAYGLTETSPAACINPLDLKDYNSSIG 382

Query: 394 KPSPAFDVKILDENGATLPPGQEGDIALQVLPERPFGLFTHYVDNPSKTASTLRGSFYI- 452
            P P+ DV I  E+   LP G+ G++ ++  P+   G    Y   P +TA  L    ++ 
Sbjct: 383 LPIPSTDVAIWSEDSQPLPIGEVGELMVKG-PQVMQG----YWKRPDETAKVLGADGWLH 437

Query: 453 TGDRGYMDEDGYFWFVARSDDIILSSGYRIGPFEVESALIEHPSIAESAVVSSPDPIRGE 512
           TGD   MD +GY + V R  D+IL SG+ + P EVE  ++ HP +AE A V  PD   GE
Sbjct: 438 TGDIARMDANGYVYIVDRKKDMILVSGFNVYPNEVEDIVMTHPGVAEVAAVGVPDEHSGE 497

Query: 513 VVKAFIVLNPDYKSHDQEQLKKEIQEHVKKTTAPYKYPRKVEFIEELPKTVSGKVKRNEL 572
           VVK F+V        D     + ++E  ++    YK P+ +EF + LPK+  GK+ R EL
Sbjct: 498 VVKLFVV------RKDPNLTVEALKEFCRENLTGYKRPKLIEFRDALPKSNVGKILRREL 551

Query: 573 RKKE 576
           R ++
Sbjct: 552 RDEK 555


Lambda     K      H
   0.319    0.134    0.416 

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: 759
Number of extensions: 35
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 580
Length of database: 562
Length adjustment: 36
Effective length of query: 544
Effective length of database: 526
Effective search space:   286144
Effective search space used:   286144
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: 53 (25.0 bits)

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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 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