GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Tistlia consotensis USBA 355

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate WP_085121636.1 B9O00_RS06430 acetyl-CoA C-acyltransferase

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



>NCBI__GCF_900177295.1:WP_085121636.1
          Length = 393

 Score =  333 bits (854), Expect = 5e-96
 Identities = 201/404 (49%), Positives = 259/404 (64%), Gaps = 14/404 (3%)

Query: 1   MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60
           M E + + AVR+ IG + GALA      LGA  ++  +AR   ++   V  V++G   Q 
Sbjct: 1   MTEVVFVSAVRSAIGTFGGALAGESPCSLGAAVVREALAR-AGVEGEQVGHVVFGNVIQT 59

Query: 61  GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120
              +  +AR+AAL  G+  + P  TLNRLCGSG  A+ SAA+++  G+A + +AGG E+M
Sbjct: 60  EPRDAYLARVAALDGGVAKAAPAMTLNRLCGSGAQAIVSAAQSILLGDAEVAVAGGAEAM 119

Query: 121 SRAPFVM--GKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISR 178
           SRAP ++  G+  Q  G +A + D  +G      ++   FG   M  TAE VA ++ I R
Sbjct: 120 SRAPHLLTTGRFGQRMGDTAAV-DALVG------ILTDPFGNGIMGLTAERVADKWGIGR 172

Query: 179 ADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKL 238
             QDAFAL SQ +AA AI  GR   +I+ +E+  R   A+    DEHP+  TT E LA L
Sbjct: 173 ERQDAFALESQRRAARAIGEGRFESQILPLEVG-RGSRARSFAVDEHPKPQTTAEDLANL 231

Query: 239 GTPFRQ-GGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGI 297
              FR+ GGSVTAGNASG+NDGA AL+L S+EAA+R G +   R+VG A AGVEP  MGI
Sbjct: 232 KPAFRRDGGSVTAGNASGINDGAAALVLMSAEAAERGGHRPLGRLVGYAHAGVEPGEMGI 291

Query: 298 GPVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGH 357
           GPVPA R +L  TGLA+ D D++E NEAFAAQ LAV  ELGL  D ERVNPNGGAIALGH
Sbjct: 292 GPVPAVRGLLARTGLAVEDFDLVESNEAFAAQALAVSDELGL--DPERVNPNGGAIALGH 349

Query: 358 PLGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401
           P+G +GA L   AL+EL    GR AL T+CIG GQGIAL +ER+
Sbjct: 350 PVGATGAILTVKALYELARSGGRRALVTLCIGGGQGIALALERL 393


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: 468
Number of extensions: 24
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: 401
Length of database: 393
Length adjustment: 31
Effective length of query: 370
Effective length of database: 362
Effective search space:   133940
Effective search space used:   133940
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