GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpE in Lentibacillus jeotgali Grbi

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 WP_010529673.1 ON01_RS03745 acyl--CoA ligase

Query= SwissProt::Q3UNX5
         (580 letters)



>NCBI__GCF_000224785.1:WP_010529673.1
          Length = 526

 Score =  388 bits (997), Expect = e-112
 Identities = 216/518 (41%), Positives = 306/518 (59%), Gaps = 11/518 (2%)

Query: 63  TNMEK-AGKRLSNPAFWWIDGNGEELRWSFEELGLLSRKFANILTEACSLQRGDRVMVIL 121
           T ME  A K     A  W    GE    ++E+L     K  N   E   L++GDRV++++
Sbjct: 16  TEMEYFAAKSPERNAVVWCSEKGESKEITYEQLMKNVNKIGNAFKEK-GLEKGDRVLIMI 74

Query: 122 PKIPEWWLANVACLRTGTVLIPGTTQLTQKDILYRLQSSKAKCIITDDTLAPAVDAVAAK 181
           P++ E +   +A L++G ++IPG+  L  KD+ YR+   +   I++     P V      
Sbjct: 75  PRLIEAYETYLAALKSGIIVIPGSEMLKTKDLQYRISHGEVSAIVS---YYPYVGQFTDV 131

Query: 182 CENLHSKLIVSQHSREGWGNLKEMMKYASDSHTCVDTKHDEMMAIYFTSGTTGPPKMIGH 241
            E     L    +S +GW N+ ++ + ASD     DT  D++    +TSGTTG PK + H
Sbjct: 132 KEFEQLTLFSVGNSVDGWHNMDKLKENASDKLDMADTTKDDVAFFSYTSGTTGNPKAVVH 191

Query: 242 THSSFGLGLSVNGRFWLDLIASDVMWNTSDTGWAKSAWSSVFSPWTQGACVFAHYLPRFE 301
           TH      L+     WL +   D +W T+  GW K  WS   S    GA  F  YL +F+
Sbjct: 192 THGWGYAHLNTAPENWLCINEGDKVWATAGPGWQKWIWSPFLSVLGSGATGFV-YLGKFD 250

Query: 302 STSILQTLSKFPITVFCSAPTAYRMLVQND-MSSYKFNSLKHCVSAGEPINPEVMEQWRK 360
             + L  L    I V C  PT YR++ + D +  Y+  +L   VSAGEP+N EV++ +RK
Sbjct: 251 PKTYLGLLQDEDINVLCCTPTEYRLMAKVDNLDDYQLPALHSAVSAGEPLNREVIDTFRK 310

Query: 361 KTGLDIYEGYGQTETVLICGNFKGMKIKPGSMGKPSPAFDVKILDENGATLPPGQEGDIA 420
              + + +GYGQTE  L+ G  K  K+KPGSMGKP+P  +V+I++E+G  +P  + GDIA
Sbjct: 311 YFNVTVRDGYGQTENTLLLGFMKDTKVKPGSMGKPTPGNEVEIINEDGQPVPANKIGDIA 370

Query: 421 LQVLPERPFGLFTHYVDNPSKTASTLRGSFYITGDRGYMDEDGYFWFVARSDDIILSSGY 480
           +++  + P  LF  Y  +  +T  + RG +Y+TGD+   DEDGYFWF  RSDDII+SSGY
Sbjct: 371 VKL--DSP-ALFREYYKDAERTRMSQRGEYYVTGDQASKDEDGYFWFEGRSDDIIISSGY 427

Query: 481 RIGPFEVESALIEHPSIAESAVVSSPDPIRGEVVKAFIVLNPDYKSHDQEQLKKEIQEHV 540
            IGPFEVE AL++HP + E AVV+SPD +RG VVKAFIVL       D + L +++Q+HV
Sbjct: 428 TIGPFEVEDALVKHPFVQECAVVASPDEVRGNVVKAFIVLQQGVNPDDPD-LVRDLQKHV 486

Query: 541 KKTTAPYKYPRKVEFIEELPKTVSGKVKRNELRKKEWV 578
           K+ TAPYKYPRK+EFI+ELPKT SGK++R ELR+ E V
Sbjct: 487 KELTAPYKYPRKIEFIDELPKTTSGKIRRVELRQNEKV 524


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: 816
Number of extensions: 45
Number of successful extensions: 6
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: 580
Length of database: 526
Length adjustment: 36
Effective length of query: 544
Effective length of database: 490
Effective search space:   266560
Effective search space used:   266560
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 24 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