GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Pseudomonas stutzeri RCH2

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate GFF1043 Psest_1076 acetyl-CoA acetyltransferases

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



>FitnessBrowser__psRCH2:GFF1043
          Length = 393

 Score =  340 bits (871), Expect = 6e-98
 Identities = 194/401 (48%), Positives = 261/401 (65%), Gaps = 10/401 (2%)

Query: 1   MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60
           M + +I+ A RT IG + G+LA+V A +LGA  ++AL+ +   ++ + VD+VI G    A
Sbjct: 1   MQDVVIVAATRTAIGSFQGSLANVPAVELGATVIRALLEK-TGIEPAQVDEVILGHVLTA 59

Query: 61  GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120
           G   +N AR A++ AGLP +VP  TLN++CGSGL AV  A +A+RCG+A +++AGG+E+M
Sbjct: 60  GA-GQNTARQASIKAGLPHAVPSMTLNKVCGSGLKAVHLAVQAIRCGDADVIIAGGMENM 118

Query: 121 SRAPFVMGKSEQAFGRS-AEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRA 179
           S AP+V+  +        A+I DT I     +       GI     TAEN+A ++ I RA
Sbjct: 119 SLAPYVLPGARTGLRMGHAQIVDTMITDGLWDAFNDYHMGI-----TAENLAEKYGIDRA 173

Query: 180 DQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLG 239
            QDAFA +SQ +AAAAI +GR   EI  V I QRKG       DE PR  TT E L  L 
Sbjct: 174 QQDAFAAQSQQRAAAAIESGRFDAEITPVMIPQRKGDPLAFARDEQPRAGTTAESLGGLR 233

Query: 240 TPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGP 299
             F++ G VTAGNAS +NDGA A++L S+  A+  GL   A++ G A AGV+P IMGIGP
Sbjct: 234 AAFKKDGCVTAGNASTLNDGAAAVVLMSASKAEALGLPVLAKIAGYANAGVDPAIMGIGP 293

Query: 300 VPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPL 359
           V ATR+ L+  G  LA++D+IE NEAFA Q L+V +ELG   D ++VN NGGAIALGHP+
Sbjct: 294 VTATRRCLDKAGWTLAELDLIEANEAFAVQALSVGKELGW--DADKVNVNGGAIALGHPI 351

Query: 360 GMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIER 400
           G SG R++ T LHE++ R  R  L T+CIG GQG+AL +ER
Sbjct: 352 GASGCRILVTLLHEMQRRDVRKGLATLCIGGGQGVALAVER 392


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: 405
Number of extensions: 21
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: 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 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