GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Pseudomonas fluorescens GW456-L13

Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate PfGW456L13_3394 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)

Query= reanno::Marino:GFF2751
         (415 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3394
          Length = 391

 Score =  312 bits (799), Expect = 1e-89
 Identities = 194/413 (46%), Positives = 251/413 (60%), Gaps = 29/413 (7%)

Query: 7   LKDAYIVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQA 66
           +KD  IVDA+RTPIG++ G+LS VRAD LG++ I  L ER  D+  + +DDV++G   Q 
Sbjct: 1   MKDIVIVDAVRTPIGKFRGSLSGVRADHLGSLVISRLLERV-DVSPTLVDDVIFGNVTQI 59

Query: 67  GEDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESM 126
           GE + ++AR +LL AG PV V G TI+R CGSG  AV  A  AI  G   +++AGG E+M
Sbjct: 60  GEQSANIARTALLGAGWPVTVAGLTIDRKCGSGEVAVHMAVGAIAAGAADIVVAGGAENM 119

Query: 127 SRAPFVMGKADSAFSRKAEIFDTTIGWRFVNPVLKKQYGIDSMPETAENVAADFGISRED 186
           SR P  MG          EI     GW     +  ++Y + S  E AE +A  + +SR+ 
Sbjct: 120 SRVP--MGS-------NREIHGAAFGW-----MAAQRYELTSQGEAAERMADKWALSRDA 165

Query: 187 QDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPL-----VVDTDEH-PRETSLEKL 240
            D FA  S QR AAA   G    E  PV +   ++  L     V+  DE   R+TS EKL
Sbjct: 166 LDDFAFASHQRAAAACDAGYFDNETIPVVVEELREKELSEPAGVLRHDETIRRDTSREKL 225

Query: 241 ASLPTPFR-ENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRI 299
           ++L T FR + G +TAGN+S ++DGA ALLL  AD  K+  LK RARVVA  T G +P +
Sbjct: 226 STLKTSFRPDTGRITAGNSSQISDGAAALLLMSADTAKKLGLKARARVVAFTTVGSDPTL 285

Query: 300 MGFGPAPATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIA 359
           M  GP  AT+KVLA AGL + D+D+ E+NEAFA+  LA  ++ G+P     +N NGGAIA
Sbjct: 286 MLTGPIAATQKVLAKAGLSINDIDLFEVNEAFASVPLAWMQETGVPH--SKLNVNGGAIA 343

Query: 360 LGHPLGMSGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIERMD 412
           LGHPLG SGARL+TT LNELERR       RY L  +C   G G A IIER+D
Sbjct: 344 LGHPLGASGARLMTTMLNELERR-----GGRYGLQAICCAGGMGTATIIERLD 391


Lambda     K      H
   0.318    0.133    0.382 

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: 25
Number of successful extensions: 7
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: 415
Length of database: 391
Length adjustment: 31
Effective length of query: 384
Effective length of database: 360
Effective search space:   138240
Effective search space used:   138240
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 (21.7 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