GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Streptacidiphilus oryzae TH49

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate WP_037570864.1 BS73_RS08675 thiolase family protein

Query= metacyc::MONOMER-15952
         (401 letters)



>NCBI__GCF_000744815.1:WP_037570864.1
          Length = 390

 Score =  292 bits (747), Expect = 1e-83
 Identities = 172/401 (42%), Positives = 237/401 (59%), Gaps = 15/401 (3%)

Query: 1   MNEALIIDAVRTPIGRY--AGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCAN 58
           M +A+I+DAVRTP+GR    GAL+ V   DL A  LKAL  R+  LD   VDDV++GC +
Sbjct: 1   MRDAVIVDAVRTPVGRGKPGGALSGVHPVDLSAHILKALAERNG-LDPGTVDDVVWGCVS 59

Query: 59  QAGEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVE 118
           Q GE    V R A L AG P  VPG T++R CGS   AV   A  +  G+  + +AGGVE
Sbjct: 60  QVGEQAGCVGRYAVLAAGWPEHVPGLTIDRQCGSSQQAVHQVAAGVIAGQYDIAVAGGVE 119

Query: 119 SMSRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISR 178
            MSR P    + + + G+    F   +G R+ +    QG G       AE +A +F  +R
Sbjct: 120 MMSRVPMGSTRGDSSQGKP---FGPLVGERYDHFRFNQGIG-------AEMIAEEFGFTR 169

Query: 179 ADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKL 238
           AD D  AL S  +AA A+A GR   +I  V +    G +++V+ DE  R   +LE+LA L
Sbjct: 170 ADLDQHALDSHARAARAVAEGRFKSQIAPVTVPTEDGGSRVVDTDEGIRPGGSLEKLAAL 229

Query: 239 GTPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIG 298
            TPF++ G ++AGN+S ++DGA ALL+ + E A+ +G    AR       G +P  M  G
Sbjct: 230 KTPFKEDGVISAGNSSQISDGAAALLITTGEVARANGWTPIARFHTGTVVGADPITMLKG 289

Query: 299 PVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHP 358
           P+PATRK+L+ +GL + D    E+NEAFA   L   RELG   D E++NPNGGA+ALGHP
Sbjct: 290 PIPATRKLLQRSGLGIGDFGAYEVNEAFAPVSLGWQRELGA--DYEKLNPNGGAMALGHP 347

Query: 359 LGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIE 399
           LG SGARL+TT +H ++    ++ L +MC G G   A ++E
Sbjct: 348 LGASGARLMTTLIHHMKANDIQFGLQSMCEGGGMANATVLE 388


Lambda     K      H
   0.319    0.134    0.384 

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: 486
Number of extensions: 21
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: 401
Length of database: 390
Length adjustment: 31
Effective length of query: 370
Effective length of database: 359
Effective search space:   132830
Effective search space used:   132830
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 (21.8 bits)
S2: 50 (23.9 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