GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_1417 N515DRAFT_1417
           long-chain acyl-CoA synthetase
          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.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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