Align D-mannonate dehydratase (EC 4.2.1.8) (characterized)
to candidate PfGW456L13_3477 Mannonate dehydratase (EC 4.2.1.8)
Query= metacyc::MONOMER-17955 (360 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3477 Length = 361 Score = 371 bits (953), Expect = e-107 Identities = 174/360 (48%), Positives = 246/360 (68%), Gaps = 13/360 (3%) Query: 1 MKLVFRWYGEKHDTVTLEQIRQIPGVEGVVGALFDIPVGEVWPFEEIMKLKETVEKAGLK 60 MK++FRW+G K D + L+ I QIPG+ G+V +L+D P+GEVWP + I L++ GLK Sbjct: 1 MKMIFRWHGPK-DPINLQYINQIPGLYGIVSSLYDTPLGEVWPVDRITSLRDAAAAYGLK 59 Query: 61 LEVIESVNVHEDIKLGLPTRDRYIENYKKTIRNLAKAGVKVVCYNFMPVFDWMRTDLHKK 120 ++V++S VHEDIKLG P R+ I Y +T++NLA +G+K+VCYNFMPVFDW RT + + Sbjct: 60 MDVVDSFRVHEDIKLGKPNREALIPQYIETLKNLAASGIKIVCYNFMPVFDWTRTQMEYQ 119 Query: 121 LPDGSETMEYDHRLIEGVTPDELIKRVKEGSQGFV-LPGWEWDR-LEKLRETFELYKNVD 178 LPDGS T+ ++ L++ + + S+G + LPG EKL+ E YK+V Sbjct: 120 LPDGSNTLSFEASLVDRL----------DVSKGVIPLPGIGTKYPAEKLQALLEEYKDVS 169 Query: 179 EEKLFENLVYFLERVIPVCEECDVKLAIHPDDPPWSIFGLPRIITNKENIERMLKAVDSP 238 E++++NL +FL +++PV E+ +KLA+H DDPP S+FGLPRII N E+ R+L +DSP Sbjct: 170 TEQMWKNLEWFLGKLVPVAEQLGLKLALHADDPPRSVFGLPRIIKNIEDHRRVLSIIDSP 229 Query: 239 YNGITFCMGSLGANPENNIPEMIRYFGKMGRIHFAHVRNLKFTGEKSFYETAHPSFCGSH 298 NG+T C G++G++ N++P I F R+H+ H+RN+K FYE+AHP+ CGS Sbjct: 230 ANGLTLCSGTIGSDLNNDVPSFINEFAARQRVHYVHLRNVKVFDNGDFYESAHPTQCGSL 289 Query: 299 DLFEVMKAFHDIGYEGYIRPDHGRLIWGEKARPGYGLYDRALGATYILGLWEAIDKMKKR 358 D+ E++KA HD + GY RPDHGR+IWGE PGYGLYDRALG Y+ GLWE I K K + Sbjct: 290 DMAEILKALHDANFTGYARPDHGRMIWGETGVPGYGLYDRALGTMYLQGLWEGIGKEKTK 349 Lambda K H 0.322 0.142 0.448 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: 437 Number of extensions: 28 Number of successful extensions: 3 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: 360 Length of database: 361 Length adjustment: 29 Effective length of query: 331 Effective length of database: 332 Effective search space: 109892 Effective search space used: 109892 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: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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:
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