GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaJ2 in Klebsiella michiganensis M5al

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate BWI76_RS23445 BWI76_RS23445 acetyl-CoA acetyltransferase

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



>lcl|FitnessBrowser__Koxy:BWI76_RS23445 BWI76_RS23445 acetyl-CoA
           acetyltransferase
          Length = 391

 Score =  313 bits (802), Expect = 5e-90
 Identities = 183/400 (45%), Positives = 257/400 (64%), Gaps = 9/400 (2%)

Query: 1   MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60
           M + +I+ A+RTPIG + G L+   A +LG++ +KAL+ R   +D  ++D+VI G    A
Sbjct: 1   MKDVVIVGALRTPIGCFQGTLSRHSAVELGSVVVKALVERSG-VDPQSIDEVILGQVLTA 59

Query: 61  GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120
           G   +N AR +A+  GLP +V   T+N +CGSGL A+  A +A++CGEA +++AGG E+M
Sbjct: 60  GT-GQNPARQSAIRGGLPNTVSAITINDVCGSGLKALHLATQAIQCGEADVVIAGGQENM 118

Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRAD 180
           SRAP V+  S       A++ ++ +    V+  +   F    M  TAEN+A ++ ISR  
Sbjct: 119 SRAPHVLTDSRTG----AQLGNSQLIDSLVHDGLWDAFNDYHMGVTAENLAREYGISREL 174

Query: 181 QDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGT 240
           QDA+AL SQHKA  AI +GR   EIV V  ++  G  ++V+ DE PR D + E LA L  
Sbjct: 175 QDAWALSSQHKARRAIDSGRFRDEIVPVT-SELNGIPRLVDTDEQPRVDPSAEALASLLP 233

Query: 241 PFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPV 300
            F Q GSVTAGNAS +NDGA A+++ S   A+  GL   AR+   A+ GV+P +MGI PV
Sbjct: 234 TFDQQGSVTAGNASSINDGAAAVMMMSETKAEALGLPILARIRAFASVGVDPALMGIAPV 293

Query: 301 PATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLG 360
            ATR+ LE  G  L ++D+IE NEAFAAQ ++V R L    D+ RVN NGGAIALGHP+G
Sbjct: 294 HATRRCLERAGWKLDEVDLIEANEAFAAQAISVGRVLEW--DERRVNVNGGAIALGHPIG 351

Query: 361 MSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIER 400
            SG R++ + +HE+ +R  R  L T+CIG GQG+AL +ER
Sbjct: 352 ASGCRILVSLVHEMIKRDARKGLATLCIGGGQGVALAVER 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: 419
Number of extensions: 16
Number of successful extensions: 5
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: 391
Length adjustment: 31
Effective length of query: 370
Effective length of database: 360
Effective search space:   133200
Effective search space used:   133200
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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