GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Phaeobacter inhibens BS107

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate GFF398 PGA1_c04090 beta-ketoadipyl-CoA thiolase PaaJ

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



>FitnessBrowser__Phaeo:GFF398
          Length = 400

 Score =  273 bits (698), Expect = 6e-78
 Identities = 170/409 (41%), Positives = 235/409 (57%), Gaps = 27/409 (6%)

Query: 3   EAVIVSTARTPIGKAYRGALNATEGATLLGHAIEH-AVKRAGIDPKEVEDVVMGAAMQQG 61
           +A I    RTPIG+ Y GAL+      L    I   A +   +D   ++DV++G A Q G
Sbjct: 2   DAFICDATRTPIGR-YGGALSQLRTDDLAALPIAALAARNPDVDWSSLDDVILGDANQAG 60

Query: 62  ATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESIS 121
            +  N+AR A L AGLP T  GTTI+R CASG+ A+ +A+R +     ++A+ GG ES+S
Sbjct: 61  ESNRNVARMAALLAGLPTTVPGTTINRLCASGMDAVGMASRGIKAGDYDMAIAGGVESMS 120

Query: 122 ---LVQNDKMNTFHAVDPALEAIKGDVYM-----------AMLDTAETVAKRYGISRERQ 167
               V     + F   +   +   G  ++           +M  TA+ VA+ YGISRE Q
Sbjct: 121 RAPFVMPKATSAFTRANAVYDTTIGWRFVNKKMHEMYGTDSMPQTADNVAEDYGISREDQ 180

Query: 168 DEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTA 227
           D ++  SQ R AAA + G FNDEI P++      D         D+ +  DE PRP T+A
Sbjct: 181 DAFAARSQARWAAAHEAGIFNDEITPVTIPQRKGD---------DLVVDTDEHPRPGTSA 231

Query: 228 EGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEP 287
           E LAGLK V G   ++TAGNAS ++DGA+A ++ ++  AA  GLKP+    GM + G EP
Sbjct: 232 EKLAGLKGVNGPDKSVTAGNASGVNDGAAAILMANEAAAAKNGLKPMARIVGMTAAGVEP 291

Query: 288 DEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGI--DPEKLNVNGGA 345
             MGIGPV A  ++L R GL++D + + ELNEAFA Q L    +LG+  D   +N NGGA
Sbjct: 292 RIMGIGPVPATRKVLARTGLTIDQMDVIELNEAFASQGLATLRELGVADDAPHVNPNGGA 351

Query: 346 ISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394
           I++GHP GMSGARL   A  + +R   +YA+ TMCVG G G+A + E V
Sbjct: 352 IALGHPLGMSGARLVLTAAYQLQRTGGRYALCTMCVGVGQGTALILERV 400


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: 420
Number of extensions: 20
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: 400
Length adjustment: 31
Effective length of query: 364
Effective length of database: 369
Effective search space:   134316
Effective search space used:   134316
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