Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate GFF964 HP15_943 aldehyde dehydrogenase family protein
Query= reanno::WCS417:GFF827 (481 letters) >FitnessBrowser__Marino:GFF964 Length = 505 Score = 288 bits (738), Expect = 2e-82 Identities = 181/477 (37%), Positives = 268/477 (56%), Gaps = 11/477 (2%) Query: 10 YING--QWVAGADYCVNLNPSELSDVIGEYAKADVTQVNAAIDAARAAFPA--WSTSGIQ 65 Y+NG QW A + +++P + + + A D + + A+ AARAAF A WS Sbjct: 30 YLNGTYQWAANGEAFTSVSPIDGRE-LASIASCDQSDADQAVMAARAAFEAGIWSQLAPA 88 Query: 66 ARHDALDKVGSEILARREELGTLLAREEGKTLPEAIG-EVTRAGNIFKFFAGECLRLSGD 124 R L + I A +EL L + GK + A +V ++ A ++ G+ Sbjct: 89 KRKAVLLRFAELIEAHGDELALLETLDMGKPINHASNVDVPATARAIRWTAEAIDKVYGE 148 Query: 125 YVPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELVPGCA 184 P+ + + ++RE +GVV I PWNFP+ + AWKIAPALA GN V++KP+E P A Sbjct: 149 LAPTPHNQIGM-ISREPMGVVAAIVPWNFPMIMAAWKIAPALATGNSVILKPSEKSPLSA 207 Query: 185 WALAEIISRAGFPAGVFNLVMGSGRVVGDVLVNSPKVDGISFTGSVGVGRQIAVSC-VSR 243 LA + AG PAGVFN++ G G VG L VD + FTGS V +Q+ + S Sbjct: 208 IRLAALAGEAGVPAGVFNVLPGYGHTVGKALALHMDVDCLVFTGSTNVAKQLMIYAGQSN 267 Query: 244 QAKVQLEMGGKNPQIILDDA-DLKQAVELSVQSAFYSTGQRCTASSRLIVTAGIHDQFVA 302 +V LE GGK+P I+ DA DLK+A + + ++ G+ CTA SRL+V I +FV Sbjct: 268 MKRVWLEAGGKSPNIVFADAPDLKKAAAEAASAIAFNQGEVCTAGSRLLVENSIRAEFVR 327 Query: 303 AMAERMKSIKVGHALKSGTDIGPVVSQAQLDQDLKYIDIGQSEGARLVSGGGLVTCDTEG 362 + E +K+ + GH L T G +V QAQLD+ + YI IGQSEGARLV GG + +T G Sbjct: 328 LICEALKTWRPGHPLDPATTCGAIVDQAQLDRIIDYIGIGQSEGARLVEGGQRILENTGG 387 Query: 363 YYLAPTLFADSEAAMRISREEIFGPVANVVRVADYEAALAMANDTEFGLSAGIATTSLKY 422 ++ PT+F MRI+ EEIFGPV +V+ + A+A+AND+ +GL+A + T+++ Sbjct: 388 LFVQPTVFDGVNNQMRIASEEIFGPVLSVIGFDTADEAVAIANDSIYGLAAAVWTSNINT 447 Query: 423 ANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSYI 479 A+ + +AG V +N G D PFGG K S G R++ +A + YT +K +++ Sbjct: 448 AHKVAKALRAGSVWINHYDGG-DMTAPFGGFKQSGNG-RDKSVHAFDKYTELKATWL 502 Lambda K H 0.318 0.134 0.390 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: 500 Number of extensions: 20 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: 481 Length of database: 505 Length adjustment: 34 Effective length of query: 447 Effective length of database: 471 Effective search space: 210537 Effective search space used: 210537 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 09 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