GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Pedobacter sp. GW460-11-11-14-LB5

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate CA265_RS17585 CA265_RS17585 acetyl-CoA acetyltransferase

Query= metacyc::MONOMER-20679
         (395 letters)



>FitnessBrowser__Pedo557:CA265_RS17585
          Length = 391

 Score =  238 bits (607), Expect = 2e-67
 Identities = 153/398 (38%), Positives = 214/398 (53%), Gaps = 14/398 (3%)

Query: 3   EAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRA-GIDPKEVEDVVMGAAMQQG 61
           EA I++  RT +GKA RG    T    L    I   V     +D ++++DV++G A  + 
Sbjct: 2   EAYIIAGYRTAVGKAPRGVFRFTRADDLAAEVIRALVASVPNLDNEQIDDVIVGNATPEA 61

Query: 62  ATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESIS 121
             G NI R   L         G T++R CASGL  IA A   +     +  + GG E +S
Sbjct: 62  EQGLNIGRMISLMGLDTDKVPGVTVNRYCASGLDTIATAVAKIKAGMADCIIAGGVEVMS 121

Query: 122 LVQNDKMNTFHAVDPALEAIKG--DVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTA 179
            +            P  E  K   D Y  M  TAE VAK Y +SRE QD +SL+S  +  
Sbjct: 122 GMPFGGWKLV----PNAEVAKNNPDWYWGMGLTAEAVAKEYNVSREDQDAFSLKSHEKAI 177

Query: 180 AAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAVRGE 239
            A + G   D I PI+     +D A      +   +  DEGPR +TT + LA LK V   
Sbjct: 178 HAIKNGHLKDGILPITVNENYLD-ANLKKKTRSYVVDTDEGPRADTTLDKLAKLKPVFDA 236

Query: 240 GFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCE---PDEMGIGPVF 296
             ++TAGN+SQ SDGA+  +++S+K       +P+     +VSYG     P  MGIGP+ 
Sbjct: 237 VGSVTAGNSSQTSDGAAFVLVVSEKKMKELNAEPIA---RLVSYGIAGVPPRIMGIGPIE 293

Query: 297 AVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGMSG 356
           A+P+ LK+ GL  +DI L ELNEAFA Q L     L ++P+ +NVNGGAI++GHP G +G
Sbjct: 294 AIPKALKQAGLKKEDIDLIELNEAFASQSLAVIRTLDLNPDVINVNGGAIALGHPLGCTG 353

Query: 357 ARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394
           A+L    + E +R+  KY +VTMCVG G G+AG+FE++
Sbjct: 354 AKLTVQIMNELKRQNKKYGMVTMCVGTGQGAAGIFELL 391


Lambda     K      H
   0.316    0.134    0.378 

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: 406
Number of extensions: 14
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: 395
Length of database: 391
Length adjustment: 31
Effective length of query: 364
Effective length of database: 360
Effective search space:   131040
Effective search space used:   131040
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 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