Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate PP_2694 PP_2694 Aldehyde dehydrogenase family protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_1109 (481 letters) >FitnessBrowser__Putida:PP_2694 Length = 480 Score = 571 bits (1472), Expect = e-167 Identities = 275/475 (57%), Positives = 354/475 (74%) Query: 5 KRYDNYINGEWVSGADYSANINPSELTDTIGDYAKADLAQVHAAIDAARAAFPAWSTSGI 64 K Y+NYI+G+W G N +PS+ D IG Y +A Q AI AARAA P W+ SG+ Sbjct: 4 KTYNNYIDGQWCEGHATLGNYSPSDTGDLIGQYHQASAEQARQAIQAARAAQPLWAASGL 63 Query: 65 QARHDSLDKVGTEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLRLSGD 124 ++R L +G E++AR+EELG LL+REEGK L E IGEV R+G F ++A E LR G+ Sbjct: 64 ESRQQVLMAIGDELIARKEELGELLSREEGKPLAEGIGEVNRSGQFFHYYAAEVLRQMGE 123 Query: 125 YLPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVLKPADLVPGCA 184 SVRPGV++EV RE +GVVG+ITPWNFP+A AWKIAPALA+GN VV KPA+LVP A Sbjct: 124 TAASVRPGVDIEVHREPVGVVGIITPWNFPMATAAWKIAPALAFGNAVVFKPANLVPASA 183 Query: 185 WALAEIISRAGFPAGVFNLVMGSGRVVGDALVQSPKVDGISFTGSVGVGRQIAVSCVSRQ 244 WAL EIISR G P+G FNLVMGSG VG+AL+QS ++D ++FTGS+ GR++AV+ Sbjct: 184 WALTEIISRQGLPSGTFNLVMGSGADVGEALIQSAEIDALTFTGSLQTGRRVAVATAGNL 243 Query: 245 AKVQLEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRFIVTAGIHDKFVEAM 304 + QLEMG KN +++DDADL+ AVE ++ AF+ TGQ+CTASSR IV GIHD+FVEA+ Sbjct: 244 VRCQLEMGSKNALVVMDDADLELAVECALNGAFFGTGQKCTASSRLIVCDGIHDRFVEAL 303 Query: 305 AERMKSIKVGHALKTGTDIGPVVSQAQLEQDLKYIDIGQSEGARLVSGGGLVACDTEGYF 364 RM+ +KVGHAL+ G IGPV QLEQ+L Y+ + Q+EGA L+ GG + +GY+ Sbjct: 304 RLRMRQLKVGHALEAGVQIGPVADARQLEQNLAYLQLAQAEGATLIEGGERLQLACDGYY 363 Query: 365 LAPTLFADSTAAMRISREEIFGPVANIVRVADYEAALAMANDTEFGLSAGIATTSLKYAN 424 + P LF +S MRI+REE+FGP+A ++RV D+E ALA NDTE+GL+AGI T SL++A+ Sbjct: 364 MRPALFINSRNDMRINREEVFGPIACVIRVRDFEEALATLNDTEYGLTAGIITQSLRHAS 423 Query: 425 HFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSYI 479 HFKR +Q G VMVNLPTAG DYHVPFGGRK SS+G REQG+YA++FYTVVKT+Y+ Sbjct: 424 HFKRRAQTGCVMVNLPTAGTDYHVPFGGRKASSFGPREQGQYARDFYTVVKTTYL 478 Lambda K H 0.318 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: 653 Number of extensions: 18 Number of successful extensions: 1 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: 480 Length adjustment: 34 Effective length of query: 447 Effective length of database: 446 Effective search space: 199362 Effective search space used: 199362 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: 51 (24.3 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