GapMind for catabolism of small carbon sources

 

Aligments for a candidate for put1 in Cupriavidus basilensis 4G11

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate RR42_RS20125 RR42_RS20125 transcriptional regulator

Query= reanno::Cup4G11:RR42_RS20125
         (1333 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS20125 RR42_RS20125 transcriptional
            regulator
          Length = 1333

 Score = 2595 bits (6726), Expect = 0.0
 Identities = 1333/1333 (100%), Positives = 1333/1333 (100%)

Query: 1    MATTTLGVKLDDASRERLKRVAQSIDRTPHWLIKQAIFTYLEQVERGNIPHETSAAGTGS 60
            MATTTLGVKLDDASRERLKRVAQSIDRTPHWLIKQAIFTYLEQVERGNIPHETSAAGTGS
Sbjct: 1    MATTTLGVKLDDASRERLKRVAQSIDRTPHWLIKQAIFTYLEQVERGNIPHETSAAGTGS 60

Query: 61   EGAADGADAFDGAASDGAIQPFLEFAQSVQPQSVLRAAITAAYRRPESECVPVLLEQARL 120
            EGAADGADAFDGAASDGAIQPFLEFAQSVQPQSVLRAAITAAYRRPESECVPVLLEQARL
Sbjct: 61   EGAADGADAFDGAASDGAIQPFLEFAQSVQPQSVLRAAITAAYRRPESECVPVLLEQARL 120

Query: 121  PHQQAEAALAMARTLATRLRERKVGTGREGLVQGLIQEFSLSSQEGVALMCLAEALLRIP 180
            PHQQAEAALAMARTLATRLRERKVGTGREGLVQGLIQEFSLSSQEGVALMCLAEALLRIP
Sbjct: 121  PHQQAEAALAMARTLATRLRERKVGTGREGLVQGLIQEFSLSSQEGVALMCLAEALLRIP 180

Query: 181  DKATRDALIRDKISGANWQSHLGQSPSVFVNAATWGLLFTGKLVATHTEAGLSKALTRII 240
            DKATRDALIRDKISGANWQSHLGQSPSVFVNAATWGLLFTGKLVATHTEAGLSKALTRII
Sbjct: 181  DKATRDALIRDKISGANWQSHLGQSPSVFVNAATWGLLFTGKLVATHTEAGLSKALTRII 240

Query: 241  GKGGEPLIRKGVDMAMRLMGEQFVTGETISEALANARKYEAEGFRYSYDMLGEAAMTEAD 300
            GKGGEPLIRKGVDMAMRLMGEQFVTGETISEALANARKYEAEGFRYSYDMLGEAAMTEAD
Sbjct: 241  GKGGEPLIRKGVDMAMRLMGEQFVTGETISEALANARKYEAEGFRYSYDMLGEAAMTEAD 300

Query: 301  AQRYLASYEQAINAIGQASRGRGIYEGPGISIKLSALHPRYSRAQHERVIGELYGRLKSL 360
            AQRYLASYEQAINAIGQASRGRGIYEGPGISIKLSALHPRYSRAQHERVIGELYGRLKSL
Sbjct: 301  AQRYLASYEQAINAIGQASRGRGIYEGPGISIKLSALHPRYSRAQHERVIGELYGRLKSL 360

Query: 361  TLLARQYDIGINIDAEEADRLEISLDLLERLCFEPELAGWNGIGFVVQGYQKRCPFVIDY 420
            TLLARQYDIGINIDAEEADRLEISLDLLERLCFEPELAGWNGIGFVVQGYQKRCPFVIDY
Sbjct: 361  TLLARQYDIGINIDAEEADRLEISLDLLERLCFEPELAGWNGIGFVVQGYQKRCPFVIDY 420

Query: 421  LIDLARRSRHRLMIRLVKGAYWDSEIKRAQVDGLEGYPVYTRKVYTDVSYVACARKLLSV 480
            LIDLARRSRHRLMIRLVKGAYWDSEIKRAQVDGLEGYPVYTRKVYTDVSYVACARKLLSV
Sbjct: 421  LIDLARRSRHRLMIRLVKGAYWDSEIKRAQVDGLEGYPVYTRKVYTDVSYVACARKLLSV 480

Query: 481  PDVIYPQFATHNAHTLAAIYQIAGHNYYPGQYEFQCLHGMGEPLYDQVVGPLADGKFNRP 540
            PDVIYPQFATHNAHTLAAIYQIAGHNYYPGQYEFQCLHGMGEPLYDQVVGPLADGKFNRP
Sbjct: 481  PDVIYPQFATHNAHTLAAIYQIAGHNYYPGQYEFQCLHGMGEPLYDQVVGPLADGKFNRP 540

Query: 541  CRIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADDTISLDELVADPVAVVEQMHADEG 600
            CRIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADDTISLDELVADPVAVVEQMHADEG
Sbjct: 541  CRIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADDTISLDELVADPVAVVEQMHADEG 600

Query: 601  ALGLPHPRIAQPRTLYGESRANSAGIDLSNEHRLASLSSALLAGTSEAVSAVPLLGTEAA 660
            ALGLPHPRIAQPRTLYGESRANSAGIDLSNEHRLASLSSALLAGTSEAVSAVPLLGTEAA
Sbjct: 601  ALGLPHPRIAQPRTLYGESRANSAGIDLSNEHRLASLSSALLAGTSEAVSAVPLLGTEAA 660

Query: 661  AGEDVNQPAPVRNPSDQRDVVGHVTEASMAEVEAALQAAVNAAPIWQATPADVRAAALER 720
            AGEDVNQPAPVRNPSDQRDVVGHVTEASMAEVEAALQAAVNAAPIWQATPADVRAAALER
Sbjct: 661  AGEDVNQPAPVRNPSDQRDVVGHVTEASMAEVEAALQAAVNAAPIWQATPADVRAAALER 720

Query: 721  AAELMEAQMQSLMGIIVREAGKTFSNAIAEVREAVDFLRYYAAQVRETFSSDTHRPLGPV 780
            AAELMEAQMQSLMGIIVREAGKTFSNAIAEVREAVDFLRYYAAQVRETFSSDTHRPLGPV
Sbjct: 721  AAELMEAQMQSLMGIIVREAGKTFSNAIAEVREAVDFLRYYAAQVRETFSSDTHRPLGPV 780

Query: 781  VCISPWNFPLAIFTGQVAAALAAGNTVLAKPAEQTPLIAAQAVRLLREAGVPAGAVQLLP 840
            VCISPWNFPLAIFTGQVAAALAAGNTVLAKPAEQTPLIAAQAVRLLREAGVPAGAVQLLP
Sbjct: 781  VCISPWNFPLAIFTGQVAAALAAGNTVLAKPAEQTPLIAAQAVRLLREAGVPAGAVQLLP 840

Query: 841  GRGETVGAALVGDARVKGVMFTGSTEVARLLQRSVAGRLDAAGRPVPLIAETGGQNAMIV 900
            GRGETVGAALVGDARVKGVMFTGSTEVARLLQRSVAGRLDAAGRPVPLIAETGGQNAMIV
Sbjct: 841  GRGETVGAALVGDARVKGVMFTGSTEVARLLQRSVAGRLDAAGRPVPLIAETGGQNAMIV 900

Query: 901  DSSALAEQVVGDVVNSAFDSAGQRCSALRVLCLQEEVADRVLEMLKGAMDELTMGNPDRL 960
            DSSALAEQVVGDVVNSAFDSAGQRCSALRVLCLQEEVADRVLEMLKGAMDELTMGNPDRL
Sbjct: 901  DSSALAEQVVGDVVNSAFDSAGQRCSALRVLCLQEEVADRVLEMLKGAMDELTMGNPDRL 960

Query: 961  STDVGPVIDEEARGNIVRHIDAMRAKGRRVHQADPNGALSAACRNGTFVSPTLIELDSIE 1020
            STDVGPVIDEEARGNIVRHIDAMRAKGRRVHQADPNGALSAACRNGTFVSPTLIELDSIE
Sbjct: 961  STDVGPVIDEEARGNIVRHIDAMRAKGRRVHQADPNGALSAACRNGTFVSPTLIELDSIE 1020

Query: 1021 ELQREVFGPVLHVVRYPRAGLDTLLAQINGTGYGLTMGIHTRIDETIEHIVERAEVGNLY 1080
            ELQREVFGPVLHVVRYPRAGLDTLLAQINGTGYGLTMGIHTRIDETIEHIVERAEVGNLY
Sbjct: 1021 ELQREVFGPVLHVVRYPRAGLDTLLAQINGTGYGLTMGIHTRIDETIEHIVERAEVGNLY 1080

Query: 1081 VNRNIVGAVVGVQPFGGEGLSGTGPKAGGPLYLHRLLSVCPLDAVARVVRASDTVGGADE 1140
            VNRNIVGAVVGVQPFGGEGLSGTGPKAGGPLYLHRLLSVCPLDAVARVVRASDTVGGADE
Sbjct: 1081 VNRNIVGAVVGVQPFGGEGLSGTGPKAGGPLYLHRLLSVCPLDAVARVVRASDTVGGADE 1140

Query: 1141 TGPVRRTLTETLATLKEWAQRESAALPGLVAACERFAAASAAGLSVTLPGPTGERNTYTL 1200
            TGPVRRTLTETLATLKEWAQRESAALPGLVAACERFAAASAAGLSVTLPGPTGERNTYTL
Sbjct: 1141 TGPVRRTLTETLATLKEWAQRESAALPGLVAACERFAAASAAGLSVTLPGPTGERNTYTL 1200

Query: 1201 LPRAAVLCLAQQETDLAVQLAAVLAAGSQAVWVESPMARALFARLPKAVQSRVRLVADWS 1260
            LPRAAVLCLAQQETDLAVQLAAVLAAGSQAVWVESPMARALFARLPKAVQSRVRLVADWS
Sbjct: 1201 LPRAAVLCLAQQETDLAVQLAAVLAAGSQAVWVESPMARALFARLPKAVQSRVRLVADWS 1260

Query: 1261 AGDTGFDAVLHHGDSDQLRAVCEQLATRPGPIISVQGLAHGEPNIAIERLLIERSLSVNT 1320
            AGDTGFDAVLHHGDSDQLRAVCEQLATRPGPIISVQGLAHGEPNIAIERLLIERSLSVNT
Sbjct: 1261 AGDTGFDAVLHHGDSDQLRAVCEQLATRPGPIISVQGLAHGEPNIAIERLLIERSLSVNT 1320

Query: 1321 AAAGGNASLMTIG 1333
            AAAGGNASLMTIG
Sbjct: 1321 AAAGGNASLMTIG 1333


Lambda     K      H
   0.318    0.133    0.383 

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: 4610
Number of extensions: 157
Number of successful extensions: 3
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: 1333
Length of database: 1333
Length adjustment: 49
Effective length of query: 1284
Effective length of database: 1284
Effective search space:  1648656
Effective search space used:  1648656
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.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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