GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Halomonas xinjiangensis TRM 0175

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate WP_043532471.1 JH15_RS16990 acetyl-CoA C-acyltransferase FadA

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



>NCBI__GCF_000759345.1:WP_043532471.1
          Length = 392

 Score =  288 bits (737), Expect = 2e-82
 Identities = 168/403 (41%), Positives = 241/403 (59%), Gaps = 22/403 (5%)

Query: 3   EALIIDAVRTPIGRYA-GALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQAG 61
           + +++D VRT + +   GA  +VRA++L A  ++AL  R+  LD + VDDVI+GC NQ  
Sbjct: 7   DIVVVDGVRTAMAKAKNGAFRNVRAENLSASVMQALFDRNAGLDPNEVDDVIWGCVNQTL 66

Query: 62  EDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESMS 121
           E + N+AR AA++ G+P SVP  T+NRLCGS + A+  AA  ++ G     + GGVE M 
Sbjct: 67  EQSMNIARNAAIMTGIPRSVPAQTVNRLCGSSMTALHIAAANIKAGMGDFYIIGGVEHME 126

Query: 122 RAPFVMGKS-EQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRAD 180
             P   G     A  + A               M  G        TAE ++    ++R D
Sbjct: 127 HVPMAHGVDVNPAASKYA-----------AKAAMMMGL-------TAELLSKMHGVTRED 168

Query: 181 QDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGT 240
           QD F +RS  +A AA   G    EIV +E    +G  ++++HDE  R D +LE++AKL  
Sbjct: 169 QDKFGVRSHQRAYAANQQGYFDNEIVGIEGHDTQGFKRLIKHDEVVRIDASLEEMAKLKP 228

Query: 241 PF-RQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGP 299
            F  + G+V+AG +S ++ GA A+ + S E AQ  GL+  ARV+    AG +  IMG GP
Sbjct: 229 VFDPRSGTVSAGTSSALSVGASAMAVMSYERAQALGLQPIARVLSTGVAGCDASIMGYGP 288

Query: 300 VPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADD-DERVNPNGGAIALGHP 358
           VPA++K L+  GL+  D+  +ELNEAFAAQ + VL++LG  D  DE+VN NGGAIALGHP
Sbjct: 289 VPASKKALKAAGLSSKDIQTVELNEAFAAQAIPVLKDLGFYDAMDEKVNLNGGAIALGHP 348

Query: 359 LGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401
           LG SG+R+ TT L+ ++++     L TMCIG+GQG+A + ER+
Sbjct: 349 LGCSGSRICTTLLNVMQQQDTTLGLATMCIGMGQGVATVFERL 391


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: 412
Number of extensions: 22
Number of successful extensions: 4
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: 392
Length adjustment: 31
Effective length of query: 370
Effective length of database: 361
Effective search space:   133570
Effective search space used:   133570
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