Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate 3609634 Dshi_3017 aldehyde dehydrogenase (RefSeq)
Query= BRENDA::P07275 (575 letters) >FitnessBrowser__Dino:3609634 Length = 780 Score = 114 bits (284), Expect = 2e-29 Identities = 126/480 (26%), Positives = 201/480 (41%), Gaps = 71/480 (14%) Query: 79 FPQTNPANHQQVLANVTQATEKDVMNAVKAAKDAKKDWYNLPFYDRSAIFLKAADLISTK 138 F NPA + LA VTQ TE D+ AV AA+ A+ W L + + A L+ Sbjct: 48 FATRNPARGTE-LAQVTQGTEADIEAAVTAARRAQPAWARLGGQGWARVLYAIARLLQKH 106 Query: 139 YRYDMLAATMLGQGKNVYQAEIDCITELSDFFRYYVKYASDLYAQQPVESADGTWNKAEY 198 R + T L GK + ++ I F Y+ A+ + + P G + Sbjct: 107 SRLFAVLET-LDNGKPIRESRDIDIPLAQRHFYYHAGMAALMEDELPDRVPVGVCGQ--- 162 Query: 199 RPLEGFVYAVSPFNFTAIAANLIGAPAL-MGNTVVWKPSQTAALSNYLLMTVLEEAGLPK 257 + P+NF + APAL MGNTVV KP++ L+ L + EAG+P Sbjct: 163 ---------IVPWNFPLLMLAWKIAPALAMGNTVVLKPAEWTPLTALLFAEICGEAGVPP 213 Query: 258 GVINFIPGDPVQVTDQVLADKDFGALHFTGSTNVFKSLYGKIQSGVVEGKYRDYPRIIGE 317 GV+N + GD +++ + FTGST+V + + ++ GK + E Sbjct: 214 GVVNIVTGDGA-TGAALVSHPGVDKIAFTGSTDVGREIR---RATAGTGK-----ALTLE 264 Query: 318 TGGKNFHLVHPSANISHAVLSTIRGTFEFQGQKCSAASRLYLPESKSEEFLSDMFGILQS 377 GGK+ ++V A++ AV + + QGQ C A SRL + E +E F + Sbjct: 265 LGGKSPYVVFEDADLDSAVEGLVDAIWFNQGQVCCAGSRLLVQEGIAEAFYA-------- 316 Query: 378 QNVVPMNTSASPISGGNLRGFMGPVIHEQSFDKLVKV---IEDAKKDPELEILYGGQYD- 433 LR M + DK + V ++ A E++ G + Sbjct: 317 ----------------KLRARMATLRIGDPLDKCIDVGAMVDPAHCAKVAEMVAGSNGEV 360 Query: 434 ------KSQGWFVGPTVIKAKRPDHPYMSTEFFGPILTVYEYPDTEFNEICDIID--NTS 485 ++G F PT+I P P M E FGP+L T F + ++ N + Sbjct: 361 HQPGTVPAEGAFYPPTLITGLEPADPLMRDEIFGPVLVA-----TTFRTPAEAVEVANAT 415 Query: 486 QYALTGAIFAKD-RKAIEYADEKLKFSAGNFYINDKCTGAVVSQQWFGGARMSGTDDKAG 544 +Y L +++++ +A++ A K +AG ++N T + FGG R SG + G Sbjct: 416 RYGLAATLWSENINRALDIAP---KLAAGVVWVN--ATNLFDAAAGFGGVRESGFGREGG 470 Score = 47.0 bits (110), Expect = 3e-09 Identities = 58/233 (24%), Positives = 104/233 (44%), Gaps = 15/233 (6%) Query: 90 VLANVTQATEKDVMNAVKAAKDAKKDWYNLPFYDRSAIFLKAADLISTKYRYDMLAATML 149 +L + + + KD+ NAV+AA A W + R+ I A+ +S + AT + Sbjct: 534 LLGHAPEGSRKDIRNAVEAATGAAS-WGRTTGHLRAQILYYVAENLSARTEE---FATRI 589 Query: 150 GQ--GKNVYQAEIDCITELSDFFRYYVKYASDLYAQQPVESADGTWNKAEYRPLEGFVYA 207 + G V +AE + + F Y A +PV E P+ G + A Sbjct: 590 AEMTGSRVPRAEAEVSAAIDRLFTYAAWADKYDGAVKPVPIRGVALAMPE--PV-GVIGA 646 Query: 208 VSPFNFTAIAA-NLIGAPALMGNTVVWKPSQTAALSNYLLMTVLEEAGLPKGVINFIPGD 266 +P + + A +++GA MGN +V PS+ L+ L VL+ + +P GV+N + G Sbjct: 647 FAPDDAPLLGAVSILGAALAMGNRLVLVPSEPFPLAATDLYQVLDTSDVPAGVVNIVTGA 706 Query: 267 PVQVTDQVLADKDFGAL-HFTG---STNVFKSLYGKI-QSGVVEGKYRDYPRI 314 + + + A+ F+G ST + G + ++ V G+ RD+ ++ Sbjct: 707 HEALAKPLASHLGVDAVWSFSGADISTTIEAEAAGNLKRTWVNHGRARDWMQV 759 Lambda K H 0.318 0.135 0.401 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: 962 Number of extensions: 37 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 575 Length of database: 780 Length adjustment: 39 Effective length of query: 536 Effective length of database: 741 Effective search space: 397176 Effective search space used: 397176 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: 54 (25.4 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