Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_011767475.1 AZO_RS18830 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA
Query= reanno::HerbieS:HSERO_RS00905 (1230 letters) >NCBI__GCF_000061505.1:WP_011767475.1 Length = 1221 Score = 1304 bits (3375), Expect = 0.0 Identities = 722/1227 (58%), Positives = 864/1227 (70%), Gaps = 23/1227 (1%) Query: 16 FQAELLPTPSPLRAAITAAYRRDEREAVQWLLQQVQEEQPWKD----ATQQLARKLVQQV 71 F A++ P LRAAITAA RRDE + V L+ ++Q+ + A + A LV V Sbjct: 3 FDADVPEAPGALRAAITAATRRDEADCVHALVAELQQRRARLGLDDAAVEARAAALVVDV 62 Query: 72 REKRTRSSGVDALMHEFSLSSEEGVALMCLAEALLRIPDRQTADRLIADKISKGDWRKHL 131 R +R + GVD LMHEFSLS++EGVALMCLAEALLRIPD TADRLI DKI +GDWR HL Sbjct: 63 RRRRRGAGGVDQLMHEFSLSTQEGVALMCLAEALLRIPDHATADRLIRDKIGQGDWRTHL 122 Query: 132 GESPSLFVNAATWGLLITGKLVSTSSESGLTQAITRLIGKGGEPLIRKGVDLAMRMLGNQ 191 G S SLFVNAATWGLLI+G+LV+T SE L A++RL+ +GGEP++R+GVD AMR+LG Q Sbjct: 123 GHSESLFVNAATWGLLISGRLVATRSERALGSALSRLLARGGEPVVRRGVDFAMRLLGQQ 182 Query: 192 FVTGQTIEEALDNSRENEKRGYRYSYDMLGEAALTMHDADAYYQSYESAIHAIGRASNGR 251 FV G+TI AL SR++E RGY +S+DMLGEAALT DA+ Y ++YE AIHAIG A+ G Sbjct: 183 FVLGETIGAALRRSRDSESRGYSHSFDMLGEAALTAADAERYTRAYEEAIHAIGAAAAGH 242 Query: 252 GIKDGPGISVKLSALHPRYSRAQHARVMSELLPRLKQLLLLAKQYDIGLNIDAEEADRLE 311 G + GPGIS+KLSALHPRY RAQ +RV +ELLPRL L+ LA+ YDIG+NIDAEEADRLE Sbjct: 243 GPRAGPGISIKLSALHPRYCRAQRSRVRAELLPRLAALMRLARGYDIGVNIDAEEADRLE 302 Query: 312 LSLDMMEVLVADPDLAGFDGLGFVVQGYQKRCPFVIDYLVDLARRNGRRLMIRLVKGAYW 371 LSLD+ E LVADP LAG+DGLGFVVQ YQKR PFVIDYLVDLA R+GRRLMIRLVKGAYW Sbjct: 303 LSLDLFEALVADPLLAGWDGLGFVVQAYQKRAPFVIDYLVDLAHRSGRRLMIRLVKGAYW 362 Query: 372 DSEIKRAQVDGLEGYPVYTRKVHTDLSYLTCAQKLLAATDVIYPQFATHNAHTLAAIYHW 431 DSEIKRAQV+G GYPVYTRK HTDL+YL CA +LLA +YPQFATHNA T+A ++ Sbjct: 363 DSEIKRAQVEGQAGYPVYTRKAHTDLAYLVCAARLLAEAGAVYPQFATHNARTVAEVHEM 422 Query: 432 AR----QHQIDNYEFQCLHGMGETLYDQVVGPDNLGKACRVYAPVGSHQTLLAYLVRRLL 487 A+ + YEFQCLHGMGE+LYD VVG LG CR+YAPVGSH+TLL YLVRRLL Sbjct: 423 AQCVGAGGTLPAYEFQCLHGMGESLYDSVVGGARLGVPCRIYAPVGSHRTLLPYLVRRLL 482 Query: 488 ENGANSSFVNQIVDEAVPLDRLVGDPIETVRAQGGLPHPAIAVPHRLYGEERKNSAGIDL 547 ENGANSSFVN+IVD+++P+ L DP++ V A PHP+I +P LYG ER+NSAG+DL Sbjct: 483 ENGANSSFVNRIVDDSMPVAALAADPLQAVLAGDVTPHPSIPLPAGLYGPERRNSAGLDL 542 Query: 548 SNEDRLQQLGQLFISMADRQWQAAPLLAADTAAQSA--QAAQLVRNPADLREVVGQVSEA 605 +++ L L ++ A +A PLL + ++A Q A+ V NPAD ++VG V EA Sbjct: 543 ASDAVLAALEAALVARAGEPRRAQPLLGSGKLDEAAARQRARPVCNPADHADIVGSVVEA 602 Query: 606 TVADVDTALRAATDYAPQWQSTPATERAAMLERAADLLEEHIAELMALAVREAGKSLPNA 665 +V+ AL AA A W + P RA L AAD E A L+++ VREAGK+ NA Sbjct: 603 LPDEVEAALAAAAAAAAGWAAVPPAARADALRAAADRFEAQQAALVSVLVREAGKTWGNA 662 Query: 666 IAEVREAVDFLRYYAIASRHDGNVLAWGPVVCISPWNFPLAIFIGEVSAALAAGNVVLAK 725 +AEVREAVDF RYYA P+VCISPWNFPLAIF+G++SAALAAG VLAK Sbjct: 663 VAEVREAVDFCRYYAQQVVTLPAPTQAAPLVCISPWNFPLAIFVGQLSAALAAGRCVLAK 722 Query: 726 PAEQTALIAHRAVQLLHEAGIPRAALQLLPGRGETVGAALTSDVRVKGVIFTGSTEVAQL 785 PA T L A AV+L+H AGIPRAALQLLPGRG +VG L D R+ GV+FTGST+VA+ Sbjct: 723 PALATPLTAALAVELMHAAGIPRAALQLLPGRGGSVGQTLARDPRIGGVLFTGSTDVARG 782 Query: 786 INRTLAQRQHDDGDGSGEHGEVPLIAETGGQNALIVDSSALAEQVVQDVLSSAFDSAGQR 845 + R LA+R G E LIAETGGQNA+IVDSSAL EQVVQDVL SAFDSAGQR Sbjct: 783 LARWLAER--------GAGPEPCLIAETGGQNAMIVDSSALLEQVVQDVLVSAFDSAGQR 834 Query: 846 CSALRILCLQEDIADRTLAMLKGAMAELRVGRPDRLSIDIGPVIDAEARQNLLDHIERMR 905 CSALR+LC+Q DIA+ L MLK AM ELR+G P L+ DIGPVID AR L H+ RM+ Sbjct: 835 CSALRVLCVQRDIAEPLLTMLKDAMGELRIGDPAALATDIGPVIDNAARDALEAHVARMQ 894 Query: 906 ASARAVHQLPLGEECQHGTFVAPTVIEIDDLAQLQREVFGPVLHVLRYRRDALPQLIDAI 965 A+ R V ++PL C++G+FVAPT+IEID + + REVFGP+LHVLR+ + L +LI +I Sbjct: 895 AAGRGVFRVPLPPACENGSFVAPTLIEIDGIGDVGREVFGPILHVLRFDAEGLDRLIASI 954 Query: 966 NATGYGLTLGVHSRIDETIEFVAQRAHVGNIYVNRNIVGAVVGVQPFGGEGKSGTGPKAG 1025 NATGYGLT G+HSRIDET+E V VGN+YVNRN+VGAVVGVQPFGGEG SGTGPKAG Sbjct: 955 NATGYGLTGGLHSRIDETVERVVAGLRVGNLYVNRNMVGAVVGVQPFGGEGLSGTGPKAG 1014 Query: 1026 GPLYLKRLQRNAQLH-EELTRAQPADVPNALLDSLLDWARTHGHERLAANGQRYHRDSLL 1084 GPLYL RL AQL L PA+ P A L L WAR G LAA SL Sbjct: 1015 GPLYLHRLLGTAQLDPAALGLVAPAE-PAAALGVLAAWARQRGDSALAARCAEDGARSLA 1073 Query: 1085 QRSLVLPGPTGERNTLGFAPRGLVLCAAGSVGTLLNQLAAAFATGNTALVDERSAAI-LP 1143 LPGPTGE NTL F RG+VLC A S LL QLAAA ATGN+AL + +AA + Sbjct: 1074 GCHCALPGPTGEANTLRFVGRGVVLCVADSAPALLAQLAAALATGNSALFEAGAAAYRVA 1133 Query: 1144 SGLPAPVRAAIRRASQLDAEPLQAALVDSHQAAHW--RARLAAREGALVPLILCGEDTTI 1201 + LP+ + + AL D A W R RLA R G LV ++ Sbjct: 1134 AELPSALGGWLGVRGHGPDPVFAVALFDGDTEAEWLLRRRLAERPGPLVAVLRADGAGRY 1193 Query: 1202 PLWRLLAERALCINTTAAGGNASLMTI 1228 PL RL+AER + INT AAGGNA+LMT+ Sbjct: 1194 PLHRLVAERVVSINTAAAGGNAALMTL 1220 Lambda K H 0.319 0.134 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: 3860 Number of extensions: 183 Number of successful extensions: 10 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: 1230 Length of database: 1221 Length adjustment: 47 Effective length of query: 1183 Effective length of database: 1174 Effective search space: 1388842 Effective search space used: 1388842 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 59 (27.3 bits)
This GapMind analysis is from Sep 24 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