Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate 7023012 Shewana3_0250 aldehyde dehydrogenase (RefSeq)
Query= reanno::WCS417:GFF827 (481 letters) >FitnessBrowser__ANA3:7023012 Length = 506 Score = 270 bits (691), Expect = 6e-77 Identities = 170/467 (36%), Positives = 249/467 (53%), Gaps = 18/467 (3%) Query: 5 QRFDNYINGQWVA--GADYCVNLNPSELSDVIGEYAKADVTQVNAAIDAARAAFPAWSTS 62 +++ N+I G+WVA DY N +P + + ++D + A+DAA AA AW + Sbjct: 17 EKYANFIGGKWVAPVNGDYFENRSPVNGQNFC-KIPRSDYRDIELALDAAHAAKDAWGKT 75 Query: 63 GIQARHDALDKVGSEILARREELGTLLAREEGKTLPEAIG-EVTRAGNIFKFFAGECLRL 121 + R + L ++ + E L E GK + E + ++ + F++FAG C+R Sbjct: 76 SVTERANLLLRIADRVEQNLEYLAVAETWENGKAVRETLNADLPLFVDHFRYFAG-CIRA 134 Query: 122 SGDYVPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELVP 181 + E LGVVG I PWNFP+ + AWKIAPALA GNCVV+KPAE P Sbjct: 135 QEGSAADIDGNTVSYHFPEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCVVLKPAEQTP 194 Query: 182 GCAWALAEIISRAGFPAGVFNLVMGSGRVVGDVLVNSPKVDGISFTGSVGVGRQIAVSCV 241 L E+I P G+ N+V G G G L S ++ ++FTGS VG I Sbjct: 195 VSILVLLELIEDL-LPPGILNVVNGFGAEAGQALATSKRIAKLAFTGSTEVGYHILKCAA 253 Query: 242 SRQAKVQLEMGGKNPQI----ILDDAD--LKQAVELSVQSAFYSTGQRCTASSRLIVTAG 295 +E+GGK+P + ++D D L +AVE + AF++ G+ CT SR+++ Sbjct: 254 ESLIPSTVELGGKSPNLYFADVMDHEDEYLDKAVE-GMLLAFFNQGEVCTCPSRVLIQES 312 Query: 296 IHDQFVAAMAERMKSIKVGHALKSGTDIGPVVSQAQLDQDLKYIDIGQSEGARLVSGGGL 355 I+D+F+ + R ++IK G+ L + T +G SQ Q D+ L Y+ IG+ EGA+++ GG L Sbjct: 313 IYDRFIEKVLARAQTIKQGNPLDTATQVGAQASQEQFDKILSYLAIGKDEGAQVLLGGSL 372 Query: 356 VTCD---TEGYYLAPTLFADSEAAMRISREEIFGPVANVVRVADYEAALAMANDTEFGLS 412 + ++GYY++PT+ MRI +EEIFGPV +V D ALA+ANDTE+GL Sbjct: 373 CQLEGDQSKGYYISPTIM-KGHNKMRIFQEEIFGPVISVTTFKDEAEALAIANDTEYGLG 431 Query: 413 AGIATTSLKYANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYG 459 AG+ T + A R QAG V +N A H FGG K S G Sbjct: 432 AGVWTRDMNRAQRLGRGIQAGRVWINCYHA-YPAHAAFGGYKKSGIG 477 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: 535 Number of extensions: 31 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: 481 Length of database: 506 Length adjustment: 34 Effective length of query: 447 Effective length of database: 472 Effective search space: 210984 Effective search space used: 210984 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