Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate 3607155 Dshi_0577 aldehyde dehydrogenase (RefSeq)
Query= reanno::pseudo1_N1B4:Pf1N1B4_1109 (481 letters) >FitnessBrowser__Dino:3607155 Length = 483 Score = 549 bits (1415), Expect = e-161 Identities = 272/472 (57%), Positives = 341/472 (72%) Query: 10 YINGEWVSGADYSANINPSELTDTIGDYAKADLAQVHAAIDAARAAFPAWSTSGIQARHD 69 YI+G W G N NPS+ TD IG YA+AD Q+ A+ AAR A PAW +GIQ RHD Sbjct: 8 YIDGAWTEGTAQIENRNPSDTTDLIGMYAQADAGQLDTALAAARRAQPAWWAAGIQKRHD 67 Query: 70 SLDKVGTEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLRLSGDYLPSV 129 L +GTE++AR +E+G LL+REEGK L E GEV RAG F +FA E LR GD SV Sbjct: 68 VLMAIGTELMARSDEIGRLLSREEGKPLAEGKGEVYRAGQFFTYFAAEALRQHGDLAESV 127 Query: 130 RPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVLKPADLVPGCAWALAE 189 RPG+ ++V REA+GVV +I+PWNFP+A PAWKIAPALA+GN VV KPA++ P A AL E Sbjct: 128 RPGIEIDVRREAVGVVAIISPWNFPVATPAWKIAPALAFGNAVVWKPANVTPASAIALTE 187 Query: 190 IISRAGFPAGVFNLVMGSGRVVGDALVQSPKVDGISFTGSVGVGRQIAVSCVSRQAKVQL 249 II+R P G+FNLV G GR VG LV+S +VD ISFTGSV VGR IA + V KVQ+ Sbjct: 188 IIARQDIPKGLFNLVAGPGRDVGQRLVESAEVDAISFTGSVPVGRGIAAAAVQNMTKVQM 247 Query: 250 EMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRFIVTAGIHDKFVEAMAERMK 309 EMG KNP I++DD DL AV + SAF TGQ+CTA+SR IV + +HD FVE + + Sbjct: 248 EMGSKNPLIVMDDCDLDLAVAHAASSAFGGTGQKCTAASRLIVHSAVHDAFVEKLVAAAR 307 Query: 310 SIKVGHALKTGTDIGPVVSQAQLEQDLKYIDIGQSEGARLVSGGGLVACDTEGYFLAPTL 369 ++KVGHAL+ GT +GPVVS++QL Q+++YI +G+ EGA L+ GG + T+GYF+AP + Sbjct: 308 AMKVGHALEDGTQLGPVVSESQLNQNMEYIGVGKDEGAELLCGGDRLEMATDGYFMAPAV 367 Query: 370 FADSTAAMRISREEIFGPVANIVRVADYEAALAMANDTEFGLSAGIATTSLKYANHFKRH 429 FA + MRI+REE+F P+ + RV Y+ ALA ANDT+FGL+AGI TTSL A+HF+ H Sbjct: 368 FAGTANDMRINREEMFAPITAVQRVDSYDEALARANDTQFGLTAGIMTTSLARASHFRAH 427 Query: 430 SQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSYIGS 481 +AG VMVNLPTAG DYHVPFGGR SS+G REQG YA EFYT VKT+Y+ + Sbjct: 428 MRAGCVMVNLPTAGTDYHVPFGGRGASSFGPREQGSYAAEFYTTVKTAYVAA 479 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: 565 Number of extensions: 15 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: 483 Length adjustment: 34 Effective length of query: 447 Effective length of database: 449 Effective search space: 200703 Effective search space used: 200703 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