Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate Ac3H11_2850 Transcriptional repressor of PutA and PutP / Proline dehydrogenase (EC 1.5.99.8) (Proline oxidase) / Delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12)
Query= reanno::acidovorax_3H11:Ac3H11_2850 (1261 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2850 Length = 1261 Score = 2471 bits (6405), Expect = 0.0 Identities = 1261/1261 (100%), Positives = 1261/1261 (100%) Query: 1 MTLPTAPFADFAPRTPLANPLRAAITAAITAATRHPEPEALAPLLAQARLPADQAAAAEQ 60 MTLPTAPFADFAPRTPLANPLRAAITAAITAATRHPEPEALAPLLAQARLPADQAAAAEQ Sbjct: 1 MTLPTAPFADFAPRTPLANPLRAAITAAITAATRHPEPEALAPLLAQARLPADQAAAAEQ 60 Query: 61 LALRIAKALRERKASAGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKATRDALIR 120 LALRIAKALRERKASAGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKATRDALIR Sbjct: 61 LALRIAKALRERKASAGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKATRDALIR 120 Query: 121 DKISHGQWDAHLGKSPSLFVNAATWGLLITGKLVATHSEGSLGNSLSRLIGKGGEPLIRK 180 DKISHGQWDAHLGKSPSLFVNAATWGLLITGKLVATHSEGSLGNSLSRLIGKGGEPLIRK Sbjct: 121 DKISHGQWDAHLGKSPSLFVNAATWGLLITGKLVATHSEGSLGNSLSRLIGKGGEPLIRK 180 Query: 181 GVDMAMRMMGEQFVTGETIDEALRNARTMEAEGFRYSYDMLGEAALTSEDAKRYYSSYEQ 240 GVDMAMRMMGEQFVTGETIDEALRNARTMEAEGFRYSYDMLGEAALTSEDAKRYYSSYEQ Sbjct: 181 GVDMAMRMMGEQFVTGETIDEALRNARTMEAEGFRYSYDMLGEAALTSEDAKRYYSSYEQ 240 Query: 241 AIHAIGKASAGRGIYEGPGISIKLSALHPRYSRAQFGRVMDELYPLVLRLTALAKQYDIG 300 AIHAIGKASAGRGIYEGPGISIKLSALHPRYSRAQFGRVMDELYPLVLRLTALAKQYDIG Sbjct: 241 AIHAIGKASAGRGIYEGPGISIKLSALHPRYSRAQFGRVMDELYPLVLRLTALAKQYDIG 300 Query: 301 LNIDAEETDRLELSLDLLERLCHEPTLAGWNGIGFVIQAYQKRCPFVIDCVVDLARRTQR 360 LNIDAEETDRLELSLDLLERLCHEPTLAGWNGIGFVIQAYQKRCPFVIDCVVDLARRTQR Sbjct: 301 LNIDAEETDRLELSLDLLERLCHEPTLAGWNGIGFVIQAYQKRCPFVIDCVVDLARRTQR 360 Query: 361 RLMVRLVKGAYWDSEIKRAQVDGLKDYPVYTRKVHTDISYIACAKKLLAAPEAVYPQFAT 420 RLMVRLVKGAYWDSEIKRAQVDGLKDYPVYTRKVHTDISYIACAKKLLAAPEAVYPQFAT Sbjct: 361 RLMVRLVKGAYWDSEIKRAQVDGLKDYPVYTRKVHTDISYIACAKKLLAAPEAVYPQFAT 420 Query: 421 HNAETVATIYQLAGSNYYAGQYEFQCLHGMGEPLYEQVVGAITAGKLGREIGKGGLGRPC 480 HNAETVATIYQLAGSNYYAGQYEFQCLHGMGEPLYEQVVGAITAGKLGREIGKGGLGRPC Sbjct: 421 HNAETVATIYQLAGSNYYAGQYEFQCLHGMGEPLYEQVVGAITAGKLGREIGKGGLGRPC 480 Query: 481 RIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADETIALDELVKSPVQVVDQQAATEGT 540 RIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADETIALDELVKSPVQVVDQQAATEGT Sbjct: 481 RIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADETIALDELVKSPVQVVDQQAATEGT 540 Query: 541 AGLPHPRIPLPAALYGAHRSNSRGLDLSNENTLTELAATLQATASHAWTAAPLLAADVPA 600 AGLPHPRIPLPAALYGAHRSNSRGLDLSNENTLTELAATLQATASHAWTAAPLLAADVPA Sbjct: 541 AGLPHPRIPLPAALYGAHRSNSRGLDLSNENTLTELAATLQATASHAWTAAPLLAADVPA 600 Query: 601 GTTQPVRNPADHNDVVGQVQEATTADVDQALVHAQAAATSWAATPPAERAAALLRTADLL 660 GTTQPVRNPADHNDVVGQVQEATTADVDQALVHAQAAATSWAATPPAERAAALLRTADLL Sbjct: 601 GTTQPVRNPADHNDVVGQVQEATTADVDQALVHAQAAATSWAATPPAERAAALLRTADLL 660 Query: 661 EERIQPLMGLLMREAGKSASNAVAEVREAVDFLRYYAAQVQSTFDNATHIPLGPVACISP 720 EERIQPLMGLLMREAGKSASNAVAEVREAVDFLRYYAAQVQSTFDNATHIPLGPVACISP Sbjct: 661 EERIQPLMGLLMREAGKSASNAVAEVREAVDFLRYYAAQVQSTFDNATHIPLGPVACISP 720 Query: 721 WNFPLAIFMGQVAAALAAGNPVLAKPAEQTPLIAAEAVRLLWQAGVPRAAVQLLPGQGET 780 WNFPLAIFMGQVAAALAAGNPVLAKPAEQTPLIAAEAVRLLWQAGVPRAAVQLLPGQGET Sbjct: 721 WNFPLAIFMGQVAAALAAGNPVLAKPAEQTPLIAAEAVRLLWQAGVPRAAVQLLPGQGET 780 Query: 781 VGARLIGDARVMGVMFTGSTEVARILQRTVAGRLDAAGRPIPLIAETGGQNAMIVDSSAL 840 VGARLIGDARVMGVMFTGSTEVARILQRTVAGRLDAAGRPIPLIAETGGQNAMIVDSSAL Sbjct: 781 VGARLIGDARVMGVMFTGSTEVARILQRTVAGRLDAAGRPIPLIAETGGQNAMIVDSSAL 840 Query: 841 VEQVVGDAVSSAFDSAGQRCSALRVLCVQEEAADRVVEMLQGAMGELRVGNPGELRVDVG 900 VEQVVGDAVSSAFDSAGQRCSALRVLCVQEEAADRVVEMLQGAMGELRVGNPGELRVDVG Sbjct: 841 VEQVVGDAVSSAFDSAGQRCSALRVLCVQEEAADRVVEMLQGAMGELRVGNPGELRVDVG 900 Query: 901 PVIDAEAQAGIAQHIEKFKAQGHRVFQHPNHVSAISAPGTFVPPTLIELNHIGELQREVF 960 PVIDAEAQAGIAQHIEKFKAQGHRVFQHPNHVSAISAPGTFVPPTLIELNHIGELQREVF Sbjct: 901 PVIDAEAQAGIAQHIEKFKAQGHRVFQHPNHVSAISAPGTFVPPTLIELNHIGELQREVF 960 Query: 961 GPVLHLVRYARSDLDQLLDQINATGYGLTQGVHTRIDETIARVVNRAHAGNVYVNRNMVG 1020 GPVLHLVRYARSDLDQLLDQINATGYGLTQGVHTRIDETIARVVNRAHAGNVYVNRNMVG Sbjct: 961 GPVLHLVRYARSDLDQLLDQINATGYGLTQGVHTRIDETIARVVNRAHAGNVYVNRNMVG 1020 Query: 1021 AVVGVQPFGGEGLSGTGPKAGGPLYLLRLLSQRPADALARTFAEADRTSPHDTERRERHL 1080 AVVGVQPFGGEGLSGTGPKAGGPLYLLRLLSQRPADALARTFAEADRTSPHDTERRERHL Sbjct: 1021 AVVGVQPFGGEGLSGTGPKAGGPLYLLRLLSQRPADALARTFAEADRTSPHDTERRERHL 1080 Query: 1081 APLATLQQWAHNQGNLALAGHCQRFAQETQSGTSRTLPGPTGERNVYTLAPRARVLCLAH 1140 APLATLQQWAHNQGNLALAGHCQRFAQETQSGTSRTLPGPTGERNVYTLAPRARVLCLAH Sbjct: 1081 APLATLQQWAHNQGNLALAGHCQRFAQETQSGTSRTLPGPTGERNVYTLAPRARVLCLAH 1140 Query: 1141 SVDDLLVQTAAVLASGGTALWPHAHAGLRAKLPTHVQAQVMLQDNTLSDGSVALDAVLHH 1200 SVDDLLVQTAAVLASGGTALWPHAHAGLRAKLPTHVQAQVMLQDNTLSDGSVALDAVLHH Sbjct: 1141 SVDDLLVQTAAVLASGGTALWPHAHAGLRAKLPTHVQAQVMLQDNTLSDGSVALDAVLHH 1200 Query: 1201 GDAPSLQAVCTTLARRPGPIVGVTALQPGAADIPLERLLIERALSVNTAAAGGNASLMTI 1260 GDAPSLQAVCTTLARRPGPIVGVTALQPGAADIPLERLLIERALSVNTAAAGGNASLMTI Sbjct: 1201 GDAPSLQAVCTTLARRPGPIVGVTALQPGAADIPLERLLIERALSVNTAAAGGNASLMTI 1260 Query: 1261 G 1261 G Sbjct: 1261 G 1261 Lambda K H 0.318 0.133 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: 4343 Number of extensions: 160 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: 1261 Length of database: 1261 Length adjustment: 48 Effective length of query: 1213 Effective length of database: 1213 Effective search space: 1471369 Effective search space used: 1471369 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: 59 (27.3 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