Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate 3609634 Dshi_3017 aldehyde dehydrogenase (RefSeq)
Query= reanno::pseudo6_N2E2:Pf6N2E2_4383 (497 letters) >FitnessBrowser__Dino:3609634 Length = 780 Score = 305 bits (782), Expect = 3e-87 Identities = 189/472 (40%), Positives = 262/472 (55%), Gaps = 33/472 (6%) Query: 23 FINGEYTDAVSGETFDCLSPVDGRLLGKIASCDVADAQRAVENARATFSSGVWSRLAPSK 82 FI G + G+TF +P G L ++ AD + AV AR + W+RL Sbjct: 36 FIGGTFQ--APGKTFATRNPARGTELAQVTQGTEADIEAAVTAARR--AQPAWARLGGQG 91 Query: 83 RKATMIRFAGLLKQHAEELALLETLDMGKPISDSLNIDVPGAAQALSWSGEAIDKLYDEV 142 + A LL++H+ A+LETLD GKPI +S +ID+P A + + + DE Sbjct: 92 WARVLYAIARLLQKHSRLFAVLETLDNGKPIRESRDIDIPLAQRHFYYHAGMAALMEDE- 150 Query: 143 AATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVVLKPSEKSPLTALR 202 L R PVGV G IVPWNFPL+M WK+ PAL+ GN+VVLKP+E +PLTAL Sbjct: 151 ---------LPDRVPVGVCGQIVPWNFPLLMLAWKIAPALAMGNTVVLKPAEWTPLTALL 201 Query: 203 IAALAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYSGESNMK 262 A + EAG+P GV+N++ G G T G AL H VD + FTGST + +++ + + K Sbjct: 202 FAEICGEAGVPPGVVNIVTGDGAT-GAALVSHPGVDKIAFTGSTDVGREIRRATAGTG-K 259 Query: 263 RIWLEAGGKSPNIVFADAPDLQAAAESAASAIAFNQGEVCTAGSRLLVERSIKDTFLPLV 322 + LE GGKSP +VF DA DL +A E AI FNQG+VC AGSRLLV+ I + F + Sbjct: 260 ALTLELGGKSPYVVFEDA-DLDSAVEGLVDAIWFNQGQVCCAGSRLLVQEGIAEAFYAKL 318 Query: 323 IEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAGHSDGAKLVAGGKRILEETG--- 379 + + G+PLD +VGA+VD V A++VAG + + G Sbjct: 319 RARMATLRIGDPLDKCIDVGAMVDPAHCAKV-----------AEMVAGSNGEVHQPGTVP 367 Query: 380 --GTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIAFDTAEQAIEIANDTPYGLAAAVWTKD 437 G + PT+ G+ A + ++EIFGPVL F T +A+E+AN T YGLAA +W+++ Sbjct: 368 AEGAFYPPTLITGLEPADPLMRDEIFGPVLVATTFRTPAEAVEVANATRYGLAATLWSEN 427 Query: 438 ISKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDKYTE 489 I++A A L AG VWVN + D A FGG ++SG GR+ YT+ Sbjct: 428 INRALDIAPKLAAGVVWVNATNLFDAAAGFGGVRESGFGREGGWEGLRAYTK 479 Score = 87.8 bits (216), Expect = 1e-21 Identities = 75/249 (30%), Positives = 104/249 (41%), Gaps = 6/249 (2%) Query: 21 RAFINGEYTDAVSGETFDCLSPVDGRLLGKIASCDVADAQRAVENARATFSSGVWSRLAP 80 + +I G+ SG + SP G LLG D + AVE A S W R Sbjct: 509 KMYIGGKQARPDSGYSRPVWSP-KGVLLGHAPEGSRKDIRNAVEAATGAAS---WGRTTG 564 Query: 81 SKRKATMIRFAGLLKQHAEELALLETLDMGKPISDSLNIDVPGAAQALSWSGEAIDKLYD 140 R + A L EE A G + + +V A L DK Sbjct: 565 HLRAQILYYVAENLSARTEEFATRIAEMTGSRVPRA-EAEVSAAIDRLFTYAAWADKYDG 623 Query: 141 EVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVVLKPSEKSPLTA 200 V P + L EPVGV+GA P + PL+ A LG AL+ GN +VL PSE PL A Sbjct: 624 AVKPVPIRGVALAMPEPVGVIGAFAPDDAPLLGAVSILGAALAMGNRLVLVPSEPFPLAA 683 Query: 201 LRIAALAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYSGESN 260 + + + +P GV+N++ G + K LA H+ VD + I+ + N Sbjct: 684 TDLYQVLDTSDVPAGVVNIVTGAHEALAKPLASHLGVDAVWSFSGADISTTIEA-EAAGN 742 Query: 261 MKRIWLEAG 269 +KR W+ G Sbjct: 743 LKRTWVNHG 751 Lambda K H 0.316 0.132 0.389 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: 1039 Number of extensions: 61 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 497 Length of database: 780 Length adjustment: 37 Effective length of query: 460 Effective length of database: 743 Effective search space: 341780 Effective search space used: 341780 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 (21.6 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