Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate Ac3H11_3961 Aldehyde dehydrogenase B (EC 1.2.1.22)
Query= reanno::Smeli:SM_b20891 (477 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3961 Length = 512 Score = 674 bits (1739), Expect = 0.0 Identities = 341/481 (70%), Positives = 391/481 (81%), Gaps = 8/481 (1%) Query: 3 LHQNLIAGEWVGGDGVA---NINPSNTDDVVGEYARASAEDAKAAIAAAKAAFPAWSRSG 59 +H NLI G W DGV N NPS+T DV+G+YA AS E A A+AAA AAFPAWS S Sbjct: 34 MHANLIGGAWT--DGVRTYQNTNPSDTRDVIGDYAVASREQALDAVAAAHAAFPAWSLST 91 Query: 60 ILERHAILKKTADEILARKDELGRLLSREEGKTLAEGIGETVRAGQIFEFFAGETLRLAG 119 +R IL +EI+ARK ELG LL+REEGKTL E IGE RA IF+FFAGE LR G Sbjct: 92 PQQRFDILDAVGNEIIARKAELGDLLAREEGKTLPEAIGEVGRAAAIFKFFAGEALRPGG 151 Query: 120 EVVPSVRPGIGVEITREPAGVVGIITPWNFPIAIPAWKLAPALCYGNTIVFKPAELVPGC 179 EV+PSVRPG+G+EITREP G +GIITPWNFPIAIPAWK+APAL YGN +VFKPAE+VPG Sbjct: 152 EVMPSVRPGVGIEITREPLGTIGIITPWNFPIAIPAWKIAPALAYGNCVVFKPAEVVPGS 211 Query: 180 SWAIVDILHRAGLPKGVLNLVMGKGSVVGQAMLDSPDVQAITFTGSTATGKRVAVASVEH 239 +WA+ DILHRAGLP GV NLVMG+GS VG +L+ + ++FTGS TG+RVA A V Sbjct: 212 AWALADILHRAGLPAGVFNLVMGRGSDVGAVLLEDERIAGVSFTGSVGTGQRVAAACVPR 271 Query: 240 NRKYQLEMGGKNPFVVLDDADLSVAVEAAVNSAFFSTGQRCTASSRIIVTEGIHDRFVAA 299 K QLEMGGKNPFVVLDDADL+VAV AA+NS FFSTGQRCTASSR+IVTEGIHDRFVAA Sbjct: 272 GAKVQLEMGGKNPFVVLDDADLNVAVGAAINSGFFSTGQRCTASSRVIVTEGIHDRFVAA 331 Query: 300 MGERIKGLVVDDALKPGTHIGPVVDQSQLNQDTDYIAIGKQEGAKLAFGGEVISRD---T 356 M E++K L VDDA K GT IGPVVD QL QD +YI IG+QEGAKLA+GGE + ++ Sbjct: 332 MVEKMKTLKVDDARKAGTDIGPVVDDRQLAQDLEYIGIGQQEGAKLAYGGEALEKNADGA 391 Query: 357 PGFYLQPALFTEATNEMRISREEIFGPVAAVIRVKDYDEALAVANDTPFGLSSGIATTSL 416 PGFYL+PALFTE T MRI+REEIFGPV +V+R K+Y+EALA+ANDTPFGL+SGIATTSL Sbjct: 392 PGFYLRPALFTETTPGMRINREEIFGPVVSVLRAKNYEEALALANDTPFGLASGIATTSL 451 Query: 417 KHATHFKRNAEAGMVMVNLPTAGVDFHVPFGGRKASSYGPREQGKYAAEFYTNVKTAYTL 476 KHATHFKR+A+AGMVMVNLPTAGVD+HVPFGGRK+SSYGPREQG+YAAEFYT VKTAYT Sbjct: 452 KHATHFKRHAQAGMVMVNLPTAGVDYHVPFGGRKSSSYGPREQGRYAAEFYTTVKTAYTQ 511 Query: 477 A 477 A Sbjct: 512 A 512 Lambda K H 0.317 0.134 0.391 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: 815 Number of extensions: 32 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: 477 Length of database: 512 Length adjustment: 34 Effective length of query: 443 Effective length of database: 478 Effective search space: 211754 Effective search space used: 211754 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: 52 (24.6 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