Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_011842150.1 RSPH17029_RS16005 aldehyde dehydrogenase
Query= reanno::Smeli:SM_b20891 (477 letters) >NCBI__GCF_000015985.1:WP_011842150.1 Length = 495 Score = 294 bits (753), Expect = 4e-84 Identities = 177/475 (37%), Positives = 269/475 (56%), Gaps = 12/475 (2%) Query: 8 IAGEWV---GGDGVANINPSNTDDVVGEYARASAEDAKAAIAAAKAAFPA--WSRSGILE 62 I G++V G+ A I P + + + A +A D A+ +A+ AF A WSR + Sbjct: 22 IDGQYVDSLSGETFACIYPGDGRPLT-DVASCNAADVDVAVRSARRAFEAGVWSRMAPAD 80 Query: 63 RHAILKKTADEILARKDELGRLLSREEGKTLAEGI-GETVRAGQIFEFFAGETLRLAGEV 121 R IL + ++ ILA ++EL L + GK +A G+ V A ++A ++ GEV Sbjct: 81 RRRILLRFSELILANREELALLETLNVGKPIANAYNGDVVSAAACIAWYAEAIDKVYGEV 140 Query: 122 VPSVRPGIGVEITREPAGVVGIITPWNFPIAIPAWKLAPALCYGNTIVFKPAELVPGCSW 181 + + + REP G+V + PWN+P+++ AWKL PAL GN+++ KPAE P + Sbjct: 141 AATAHD-MTTLVMREPLGIVAAVVPWNYPMSMAAWKLGPALATGNSVILKPAEQSPFTAL 199 Query: 182 AIVDILHRAGLPKGVLNLVMGKGSVVGQAMLDSPDVQAITFTGSTATGKRVAVASVEHN- 240 ++ AG+P GVLN+V G G + G+A+ DV + FTGST GK S + N Sbjct: 200 KFGELAIEAGMPPGVLNVVPGLGHIAGKALGLHMDVDCVGFTGSTEVGKYFMQYSGQSNI 259 Query: 241 RKYQLEMGGKNPFVVLDDAD-LSVAVEAAVNSAFFSTGQRCTASSRIIVTEGIHDRFVAA 299 ++ LE+GGK+P VVL D D L A F +TGQ C A SR+IV E IHD+ + Sbjct: 260 KRIGLELGGKSPQVVLADCDDLDAAAAGIAAGIFANTGQVCNAGSRLIVDEKIHDQLLEK 319 Query: 300 MGERIKGLVVDDALKPGTHIGPVVDQSQLNQDTDYIAIGKQEGAKLAFGGEVISRDTPGF 359 + + K D L T +G +V + Q+++ YI G+ +GA+ GG + +T GF Sbjct: 320 IAAQAKVFAPGDPLDTATRMGSMVSEEQMDRVLGYIDAGRADGARPVIGGGRVKTETGGF 379 Query: 360 YLQPALFTEATNEMRISREEIFGPVAAVIRVKDYDEALAVANDTPFGLSSGIATTSLKHA 419 Y++P +F N+M+I++EEIFGPV + I VK +DEA+AVANDT +GL+ + T S+K+A Sbjct: 380 YIEPTIFEGVRNDMKIAQEEIFGPVLSAIPVKGFDEAMAVANDTVYGLAGAVWTGSVKNA 439 Query: 420 THFKRNAEAGMVMVNLPTAGVDFHVPFGGRKASSYGPREQGKYAAEFYTNVKTAY 474 ++ AG+V VN G VPFGG K S +G R++ +A + YT++K + Sbjct: 440 HRAAKSLRAGVVWVNCFDRG-SLAVPFGGFKQSGFG-RDKSLHAMDKYTDLKAVW 492 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: 574 Number of extensions: 30 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: 477 Length of database: 495 Length adjustment: 34 Effective length of query: 443 Effective length of database: 461 Effective search space: 204223 Effective search space used: 204223 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 Apr 10 2024. 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