GapMind for catabolism of small carbon sources

 

Alignments for a candidate for put1 in Pseudomonas fluorescens GW456-L13

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate PfGW456L13_223 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::pseudo3_N2E3:AO353_12810
         (1317 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_223
          Length = 1316

 Score = 2478 bits (6422), Expect = 0.0
 Identities = 1255/1317 (95%), Positives = 1288/1317 (97%), Gaps = 1/1317 (0%)

Query: 1    MATTTLGVKLDDPTRERLKAAATSIDRTPHWLIKQAIFNYLEKLEGGATLTELSGLTRSE 60
            MATTTLGVKLDDPTRERLKAAATSIDRTPHWLIKQAIFNYLEKLEGGATL+EL+G T+ +
Sbjct: 1    MATTTLGVKLDDPTRERLKAAATSIDRTPHWLIKQAIFNYLEKLEGGATLSELNGSTK-D 59

Query: 61   ADEGAEVHVDHAHQCFLEFAESILPQSVLRASITAAYRRPEPEVVPMLIEQARLPAPMAE 120
            +D+  +  +DHAHQCFLEFAESILPQSVLRASITAAYRRPEPEVVPMLIEQARLPAPMAE
Sbjct: 60   SDDSVDAPLDHAHQCFLEFAESILPQSVLRASITAAYRRPEPEVVPMLIEQARLPAPMAE 119

Query: 121  ATNKLAASIAEKLRNQKSAGGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKGTRD 180
            ATNKLAASIAEKLRNQKSAGGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKGTRD
Sbjct: 120  ATNKLAASIAEKLRNQKSAGGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKGTRD 179

Query: 181  ALIRDKISTGNWQPHLGNSPSLFVNAATWGLLLTGKLVATHNEAGLTSSLSRIIGKSGEP 240
            ALIRDKISTGNWQPHLGNSPSLFVNAATWGLLLTGKLV+THNEAGLTSSLSRIIGKSGEP
Sbjct: 180  ALIRDKISTGNWQPHLGNSPSLFVNAATWGLLLTGKLVSTHNEAGLTSSLSRIIGKSGEP 239

Query: 241  MIRKGVDMAMRLMGEQFVTGETIAEALANASKFEAKGFRYSYDMLGEAALTEHDAQKYLA 300
            MIRKGVDMAMRLMGEQFVTGETIAEALANASKFE KGFRYSYDMLGEAALTEHDAQKYLA
Sbjct: 240  MIRKGVDMAMRLMGEQFVTGETIAEALANASKFETKGFRYSYDMLGEAALTEHDAQKYLA 299

Query: 301  SYEQAIHSIGKASHGRGIYEGPGISIKLSALHPRYSRAQYERVMDELYPRLLSLTLLAKQ 360
            SYEQAIHSIGKASHGRGIYEGPGISIKLSALHPRYSRAQYERVMDELYPRLLSLTLLAKQ
Sbjct: 300  SYEQAIHSIGKASHGRGIYEGPGISIKLSALHPRYSRAQYERVMDELYPRLLSLTLLAKQ 359

Query: 361  YDIGLNIDAEEADRLELSLDLLERLCFEPQLTGWNGIGFVIQAYQKRCPYVIDYVIDLAR 420
            YDIGLNIDAEEADRLELSLDLLERLCFEPQLTGWNGIGFVIQAYQKRCPYVIDYVIDLAR
Sbjct: 360  YDIGLNIDAEEADRLELSLDLLERLCFEPQLTGWNGIGFVIQAYQKRCPYVIDYVIDLAR 419

Query: 421  RSRHRLMIRLVKGAYWDSEIKRAQVEGLEGYPVYTRKVYTDVSYIACARKLLSVPEVIYP 480
            RSRHRLMIRLVKGAYWDSEIKRAQVEGLEGYPVYTRKVYTDVSYIACARKLLSVPEVIYP
Sbjct: 420  RSRHRLMIRLVKGAYWDSEIKRAQVEGLEGYPVYTRKVYTDVSYIACARKLLSVPEVIYP 479

Query: 481  QFATHNAHTLSAIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGKVSEGKLNRPCRVYAP 540
            QFATHNAHTLSAIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGKVSEGKLNRPCRVYAP
Sbjct: 480  QFATHNAHTLSAIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGKVSEGKLNRPCRVYAP 539

Query: 541  VGTHETLLAYLVRRLLENGANTSFVNRIADQSISIQELVADPVSSIEQMATLEGGFGLPH 600
            VGTHETLLAYLVRRLLENGANTSFVNRIADQSISIQELVADPV+SIEQMAT+EGGFGLPH
Sbjct: 540  VGTHETLLAYLVRRLLENGANTSFVNRIADQSISIQELVADPVASIEQMATVEGGFGLPH 599

Query: 601  PRIPLPRDLYGSERANSSGIDLANEHRLASLSCALLATAHNNWKAAPMLGCAASAETPVP 660
            PRIPLPRDLYGSERANSSGID+ANEHRLASLSCALLATAHN+WKAAPMLGCA+S+E P P
Sbjct: 600  PRIPLPRDLYGSERANSSGIDMANEHRLASLSCALLATAHNHWKAAPMLGCASSSEAPAP 659

Query: 661  VLNPSDLRDVVGHVQEATVTDADNAIQCALNAAPIWQATPPAERAAILERAADLMESEIQ 720
            VLNPSDLRDVVGHVQEATV D DNAIQCALNAAPIWQATPPAERAAILERAADLME+EIQ
Sbjct: 660  VLNPSDLRDVVGHVQEATVEDVDNAIQCALNAAPIWQATPPAERAAILERAADLMEAEIQ 719

Query: 721  PLMGLLAREAGKTFANAIAEVREAVDFLRYYAVQARNDFTNDAHRPLGPVVCISPWNFPL 780
            PLMGLLAREAGKTFANAIAEVREAVDFLRYYAVQARNDFTNDAHRPLGPVVCISPWNFPL
Sbjct: 720  PLMGLLAREAGKTFANAIAEVREAVDFLRYYAVQARNDFTNDAHRPLGPVVCISPWNFPL 779

Query: 781  AIFSGQVAAALAAGNPVLAKPAEQTPLVAAQAVRILLEAGIPEGVLQLLPGRGETVGARL 840
            AIFSGQVAAALAAGNPVLAKPAEQTPLVAAQAVR++LEAGIPEGVLQLLPGRGETVGA L
Sbjct: 780  AIFSGQVAAALAAGNPVLAKPAEQTPLVAAQAVRLMLEAGIPEGVLQLLPGRGETVGAGL 839

Query: 841  VGDDRVKGVMFTGSTEVARLLQRNVAGRLDAQGRPIPLIAETGGQNAMIVDSSALTEQVV 900
            VGDDRVKGVMFTGSTEVARLLQRN+AGRLD+QGRPIPLIAETGGQNAMIVDSSALTEQVV
Sbjct: 840  VGDDRVKGVMFTGSTEVARLLQRNIAGRLDSQGRPIPLIAETGGQNAMIVDSSALTEQVV 899

Query: 901  IDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAECRLGNPERLSVDIGPVIDA 960
            IDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAE RLGNPERLSVDIGPVIDA
Sbjct: 900  IDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAESRLGNPERLSVDIGPVIDA 959

Query: 961  EAKAGIEKHIQAMRDKGRNVYQVAIADMEECKRGTFVMPTLIELESFDELQREIFGPVLH 1020
            EAKAGIEKHIQAMRDKGR+VYQVAIAD EE KRGTFV+PTLIELESFDELQREIFGPVLH
Sbjct: 960  EAKAGIEKHIQAMRDKGRSVYQVAIADAEEVKRGTFVIPTLIELESFDELQREIFGPVLH 1019

Query: 1021 VVRYKRKDIDQLIGQINASGYGLTLGVHTRIDETIAKVIDNVNAGNVYVNRNIVGAVVGV 1080
            VVRYKRKDIDQLIGQINASGYGLTLGVHTRIDETIAKVIDNVNAGNVYVNRNIVGAVVGV
Sbjct: 1020 VVRYKRKDIDQLIGQINASGYGLTLGVHTRIDETIAKVIDNVNAGNVYVNRNIVGAVVGV 1079

Query: 1081 QPFGGEGLSGTGPKAGGPLYLYRLLSTRPTDAIEQSFARGDTLSAPDVRLRDAMSKPLTA 1140
            QPFGGEGLSGTGPKAGGPLYLYRLLSTRP DAIEQSFARGD  +APDVRLRDAMSKPLTA
Sbjct: 1080 QPFGGEGLSGTGPKAGGPLYLYRLLSTRPADAIEQSFARGDAAAAPDVRLRDAMSKPLTA 1139

Query: 1141 LKTWADSHKLTELSALCAQFATQSQSGITRTLNGPTGERNSYAILPREHVLCLAEVESDL 1200
            LK WAD+HK  +LS LC QFA QSQSGITR L GPTGERNSYAILPREHVLCLAEVE DL
Sbjct: 1140 LKAWADNHKFADLSTLCVQFAAQSQSGITRLLAGPTGERNSYAILPREHVLCLAEVEGDL 1199

Query: 1201 LSQLAAVLAVGGSAVWPEGELSKALLARLPKDVQARIKLVADWNKDEVVFDAVLHHGHSD 1260
            L+QLAAVLAVGGSAVWPE +++KAL ARLPKD+QARIKLV+DWNKDEVVFDAVLHHGHSD
Sbjct: 1200 LTQLAAVLAVGGSAVWPEADMTKALFARLPKDIQARIKLVSDWNKDEVVFDAVLHHGHSD 1259

Query: 1261 QLRAVCQQVAKRAGAIIGVQGLSQGETNIALERLVIERALSVNTAAAGGNASLMTIG 1317
            QLRAVCQQ+AKRAGAI+GVQGLSQGETNIALERLVIERALSVNTAAAGGNASLMTIG
Sbjct: 1260 QLRAVCQQIAKRAGAIVGVQGLSQGETNIALERLVIERALSVNTAAAGGNASLMTIG 1316


Lambda     K      H
   0.318    0.134    0.386 

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: 4485
Number of extensions: 149
Number of successful extensions: 2
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: 1317
Length of database: 1316
Length adjustment: 48
Effective length of query: 1269
Effective length of database: 1268
Effective search space:  1609092
Effective search space used:  1609092
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 (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:

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. 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