Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_110805920.1 C8J30_RS10945 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA
Query= reanno::Phaeo:GFF1160
(1158 letters)
>NCBI__GCF_003217355.1:WP_110805920.1
Length = 1127
Score = 1274 bits (3297), Expect = 0.0
Identities = 692/1130 (61%), Positives = 818/1130 (72%), Gaps = 21/1130 (1%)
Query: 33 YVDQAQMRDQLFALANLDATDRSTISANAAALVRDIRGHSSPGLMEVFLAEYGLSTDEGV 92
+ +A++ + L A A L I+A A LV IR + P LME FLA+YGLST EGV
Sbjct: 13 FAPEAEVLEALVAQAALPQAQLDRIAARGADLVARIRAEAKPSLMEHFLAQYGLSTREGV 72
Query: 93 ALMCLAEALLRVPDADTIDALIEDKIAPSEWGKHLGKSTSSLVNASTWALMLTGKVLDEK 152
ALMCLAEA+LRVPD TIDALIEDKIAPS+WGKHLG + SSLVNASTWALMLTGKVLD+
Sbjct: 73 ALMCLAEAMLRVPDNATIDALIEDKIAPSDWGKHLGTAASSLVNASTWALMLTGKVLDDG 132
Query: 153 RSPVSA-LRGAMKRLGEPVIRTAVSRAMKEMGRQFVLGETIEGAMKRAAGMEAKGYTYSY 211
++ LRGAM+RLGEPVIR AV +AM+EMGRQFVLGETIE A++RA E++GYT+SY
Sbjct: 133 AGGLAGTLRGAMRRLGEPVIRAAVGQAMREMGRQFVLGETIEKALERAEKRESEGYTFSY 192
Query: 212 DMLGEAARTEADAARYHLAYSRAISAIAAACNSADIRQNPGISVKLSALHPRYELAQETS 271
DMLGEAA T ADA RY +AY++AI++IA A I NPGIS+KLSALHPRYE+AQE
Sbjct: 193 DMLGEAALTTADAERYRVAYAQAIASIAKAATKGSIAANPGISIKLSALHPRYEVAQEAR 252
Query: 272 VKEQLVPRLQALALLAKAAGMGLNVDAEEADRLSLSLEVIEEVISDPALAGWDGFGVVVQ 331
V +LVP ++ LA A AAG+ L++DAEE DRL+LSL VIE V++DP AGW GFG VVQ
Sbjct: 253 VMAELVPVVRDLARAAAAAGIALHIDAEEQDRLALSLRVIEAVMADPETAGWQGFGAVVQ 312
Query: 332 AYGPRTGAALDALYDMANRYDRRLMVRLVKGAYWDTEVKRAQVEGVDGFPVFTHKSLTDV 391
AYG R GAA+DAL MA RR+ +RLVKGAYWD+E+KRAQVEG GFP+FT K+ TDV
Sbjct: 313 AYGKRAGAAIDALAAMARASGRRINIRLVKGAYWDSEMKRAQVEGHPGFPLFTSKTGTDV 372
Query: 392 SYIANARKLLSITDRIYPQFATHNAHTVSAILHMAKDTDKGAYEFQRLHGMGETLHNMVL 451
+YI A KL ++D +YPQFATHNAHTV+A+L MA YEFQRLHGMG LH++VL
Sbjct: 373 AYICLAAKLFGLSDCLYPQFATHNAHTVAAVLEMAAGR---PYEFQRLHGMGARLHDIVL 429
Query: 452 EQNQTHCRIYAPVGAHRDLLAYLVRRLLENGANSSFVNQIVDENVPPELVAADPFAQVED 511
+ CRIYAPVGAHRDLLAYLVRRLLENGANSSFVNQIV+E+VPP VAA PFA +
Sbjct: 430 RETGGRCRIYAPVGAHRDLLAYLVRRLLENGANSSFVNQIVNESVPPSEVAACPFAALAT 489
Query: 512 LTA--NLRKGPDLFQPERPNSIGFDLGHAPTLAAIDAARAPWKSHSWAAEPLLAKAPETA 569
A L LF +R NS GFDL LA I+ AR A P++A P +
Sbjct: 490 ARAPRGLLAPAALFGSDRVNSQGFDLSDPEVLARIETARTVTLPD---AAPIVA-GPVSG 545
Query: 570 TTTDEPVRNPADLTTVGRVQTAGQAEIETALSAATPWNASAETRAEVLNRAADLYEANYG 629
+ D V NPA V RV A A + AL AA W+A A RA VL+RAADLYE N+G
Sbjct: 546 GSRD--VVNPATGAVVARVTEADAATVAVALDAARVWSAPAAERAAVLSRAADLYEENFG 603
Query: 630 ELFALLTREAGKTLPDCVAELREAVDFLRYYAARISAE--PPVGVFTCISPWNFPLAIFS 687
+FA L REAGKTL D ++ELREAVDFLRYYAA +++ P G ISPWNFPLAIF+
Sbjct: 604 PIFAALAREAGKTLGDAISELREAVDFLRYYAAEGTSDTRAPRGPVVAISPWNFPLAIFT 663
Query: 688 GQIAAALAVGNAVLAKPAEQTPLIAHRAISLLHEAGVPRSALQLLPGAG-AVGGALTSDA 746
GQIAAAL GNAVLAKPAEQTP+IA A+ LLH+AGVP +ALQLLPG G VG ALT D
Sbjct: 664 GQIAAALMAGNAVLAKPAEQTPVIAALAVRLLHQAGVPATALQLLPGDGPTVGAALTRDP 723
Query: 747 RVGGVAFTGSTATALKIRAAMAEHLRPGAPLIAETGGLNAMIVDSTALPEQAVQSIIESA 806
R+ GV FTGST TA I AMA H+ PG PLIAETGGLNAM+VDSTALPEQAV+ ++ SA
Sbjct: 724 RIKGVVFTGSTETAQIIARAMAAHMAPGTPLIAETGGLNAMVVDSTALPEQAVRDVVASA 783
Query: 807 FQSAGQRCSALRCLYLQEDIADNVLKMLKGAMDALHLGDPWNLSTDSGPVIDETARAGIL 866
F+SAGQRCSALRCLY+QEDIA +V+ MLKGAMD L LGDPW LSTD GPVID A+AGI
Sbjct: 784 FRSAGQRCSALRCLYVQEDIAPHVIAMLKGAMDELVLGDPWRLSTDVGPVIDAEAQAGIE 843
Query: 867 AHIDAARAEGRVLKEMTAPQGGTFVAPTLIEITGIQALEQEIFGPVLHVVRFKSQDLDQI 926
++ A+ GR+L AP GG FVAP L+++TGI L EIFGPVLH+ F + DL +
Sbjct: 844 TYL--AQNAGRILHRTAAPAGGHFVAPALLKVTGIADLSHEIFGPVLHLATFAADDLPAV 901
Query: 927 IRDINATGYGLTFGLHTRIDDRVQYICDRIHAGNLYVNRNQIGAIVGSQPFGGEGLSGTG 986
I INA GYGLTFGLH+RID RV+ + + I AGN+YVNRNQIGA+VGSQPFGGEGLSGTG
Sbjct: 902 IAAINARGYGLTFGLHSRIDARVETVAETIRAGNIYVNRNQIGAVVGSQPFGGEGLSGTG 961
Query: 987 PKAGGPFYMMRFCAPDRQKSVDSWPSDAPAMTMLPAPTGQPMQEITTSLPGPTGESNRLS 1046
PKAGGP Y+ RF AP+ + +W +LP + E+ LPGPTGE NRL+
Sbjct: 962 PKAGGPLYLGRFYAPEPVVATGAWTQ--AVTPVLPEAVETLLGEL--FLPGPTGELNRLT 1017
Query: 1047 QLARPPLLCLGPGPQAVVAQARAVHALGGTAIEATGPLDMRQLLTMEGTSGVIWWGDETT 1106
+ R P+LCLGPGP+A AQA AV LGG A++ATG + + L T E + V+WWG+
Sbjct: 1018 RHVRGPVLCLGPGPEAAAAQAAAVAVLGGQAVQATGAVAAKALGTAEPLAAVLWWGEAEM 1077
Query: 1107 AREIESWLARRNGPILPLIPGLPDKARVQAERHVCVDTTAAGGNAALLGG 1156
R LA R GP++PLI PD A V ERH+CVDTTAAGGNAALL G
Sbjct: 1078 GRAYAQALAARPGPLVPLITARPDLAHVAHERHLCVDTTAAGGNAALLAG 1127
Lambda K H
0.317 0.132 0.387
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: 3133
Number of extensions: 128
Number of successful extensions: 9
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: 1158
Length of database: 1127
Length adjustment: 46
Effective length of query: 1112
Effective length of database: 1081
Effective search space: 1202072
Effective search space used: 1202072
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: 58 (26.9 bits)
Align candidate WP_110805920.1 C8J30_RS10945 (bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA)
to HMM TIGR01238 (delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))
# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file: ../tmp/path.carbon/TIGR01238.hmm
# target sequence database: /tmp/gapView.1952976.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR01238 [M=500]
Accession: TIGR01238
Description: D1pyr5carbox3: delta-1-pyrroline-5-carboxylate dehydrogenase
Scores for complete sequences (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Sequence Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
1.6e-184 600.0 3.8 1.6e-184 600.0 3.8 2.2 2 NCBI__GCF_003217355.1:WP_110805920.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003217355.1:WP_110805920.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 600.0 3.8 1.6e-184 1.6e-184 2 496 .. 502 974 .. 501 977 .. 0.94
2 ! 2.8 0.5 0.0017 0.0017 221 271 .. 1047 1097 .. 1033 1118 .. 0.86
Alignments for each domain:
== domain 1 score: 600.0 bits; conditional E-value: 1.6e-184
TIGR01238 2 lygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvseadaa 74
l+g+ r ns+G dl+ ++l+++e+ + ++ +aapiv+ ++ +g + v+npa +v +v+eadaa
NCBI__GCF_003217355.1:WP_110805920.1 502 LFGSDRVNSQGFDLSDPEVLARIETARTVTL---PDAAPIVA-GPV-SGGSRDVVNPATG-AVVARVTEADAA 568
89*******************9997655444...579****4.444.56667899**975.689********* PP
TIGR01238 75 evqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflryyak 147
+v a+d+a +wsa +a+eraa+l+r+adl e++ + a l reaGktl +ai+e+reavdflryya
NCBI__GCF_003217355.1:WP_110805920.1 569 TVAVALDAA----RVWSA-PAAERAAVLSRAADLYEENFGPIFAALAREAGKTLGDAISELREAVDFLRYYAA 636
999888876....68997.999**************************************************9 PP
TIGR01238 148 qvedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqeaGvpagvi 220
+ ++ ++G+vv+ispwnfplaiftGqiaaal+aGn+v+akpaeqt++iaa av ll++aGvpa+++
NCBI__GCF_003217355.1:WP_110805920.1 637 EG----TSDTRAPRGPVVAISPWNFPLAIFTGQIAAALMAGNAVLAKPAEQTPVIAALAVRLLHQAGVPATAL 705
99....6778899************************************************************ PP
TIGR01238 221 qllpGrGedvGaaltsderiaGviftGstevarlinkalakredapvpliaetGGqnamivdstalaeqvvad 293
qllpG G +vGaalt d+ri+Gv+ftGste+a+ i +a+a ++ +pliaetGG nam+vdstal+eq v+d
NCBI__GCF_003217355.1:WP_110805920.1 706 QLLPGDGPTVGAALTRDPRIKGVVFTGSTETAQIIARAMAAHMAPGTPLIAETGGLNAMVVDSTALPEQAVRD 778
************************************************************************* PP
TIGR01238 294 vlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeakqnllahiekmka 366
v+asaf saGqrcsalr l+vqed+a +v+ ++kGamdel++g p rl tdvGpvidaea+ +++++ + +
NCBI__GCF_003217355.1:WP_110805920.1 779 VVASAFRSAGQRCSALRCLYVQEDIAPHVIAMLKGAMDELVLGDPWRLSTDVGPVIDAEAQAGIETYLAQ--N 849
*****************************************************************99864..4 PP
TIGR01238 367 kakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGygltlGvh 439
++ +++ g fvap l+++ +++l++e+fGpvlh+ + ad+l v+ ina+Gyglt+G+h
NCBI__GCF_003217355.1:WP_110805920.1 850 AGRILHRTAAP-----AGGHFVAPALLKVTGIADLSHEIFGPVLHLATFAADDLPAVIAAINARGYGLTFGLH 917
55666655444.....589****************************************************** PP
TIGR01238 440 srieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrlt 496
sri+ v + + +++Gn+yvnrn++GavvG qpfGGeGlsGtGpkaGGplyl r+
NCBI__GCF_003217355.1:WP_110805920.1 918 SRIDARVETVAETIRAGNIYVNRNQIGAVVGSQPFGGEGLSGTGPKAGGPLYLGRFY 974
*****************************************************9985 PP
== domain 2 score: 2.8 bits; conditional E-value: 0.0017
TIGR01238 221 qllpGrGedvGaaltsderiaGviftGstevarlinkalakredapvplia 271
q + G+ al + e +a v++ G +e+ r +ala r + vpli+
NCBI__GCF_003217355.1:WP_110805920.1 1047 QAVQATGAVAAKALGTAEPLAAVLWWGEAEMGRAYAQALAARPGPLVPLIT 1097
677788998889************************************996 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (500 nodes)
Target sequences: 1 (1127 residues searched)
Passed MSV filter: 1 (1); expected 0.0 (0.02)
Passed bias filter: 1 (1); expected 0.0 (0.02)
Passed Vit filter: 1 (1); expected 0.0 (0.001)
Passed Fwd filter: 1 (1); expected 0.0 (1e-05)
Initial search space (Z): 1 [actual number of targets]
Domain search space (domZ): 1 [number of targets reported over threshold]
# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 54.67
//
[ok]
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