Alignments for a candidate for put1 in Methylobacterium nodulans ORS 2060

GapMind for catabolism of small carbon sources

Alignments for a candidate for put1 in Methylobacterium nodulans ORS 2060

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_015928132.1 MNOD_RS06935 trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase

Query= reanno::azobra:AZOBR_RS23695
         (1235 letters)



>NCBI__GCF_000022085.1:WP_015928132.1
          Length = 1231

 Score = 1593 bits (4124), Expect = 0.0
 Identities = 832/1222 (68%), Positives = 953/1222 (77%), Gaps = 11/1222 (0%)

Query: 18   FADFAPPIRPATELRAAITAAYRRPEPECLPFLFEQASLPPGVITAAAATARKLITALRA 77
            F  F    R  T LRAA+TAAYRRPE EC+  L   A+LP     A A TA +L+ ALR 
Sbjct: 15   FGRFIAGTRHQTGLRAAVTAAYRRPEGECVQALLPLAALPEAQARAVAGTAERLVRALRE 74

Query: 78   KPRGRGVEGLIHEYSLSSQEGMALMCLAEALLRIPDHATRDALIRDKIAGGDWQAHLGKG 137
            K R  GVEGLIHEY+LSSQEG+ALMCLAEALLRIPD ATRDALIRDKIA GDW++H+G  
Sbjct: 75   KKRSGGVEGLIHEYALSSQEGVALMCLAEALLRIPDDATRDALIRDKIATGDWKSHVGHS 134

Query: 138  GSMFVNAATWGLLITGKLTSAGGEQALSSALTRLIARGGEPLIRRGVDFAMRMMGEQFVT 197
             S+FVNAATWGL++TGKLT+   E +LS++LTRLIA+GGEPLIRRG D AMR+MGEQFVT
Sbjct: 135  PSLFVNAATWGLVVTGKLTATTSESSLSASLTRLIAKGGEPLIRRGTDLAMRLMGEQFVT 194

Query: 198  GQTIQEALTNARTMEAEGFRYSYDMLGEAALTAEDAARYYADYVNAIHAIGTASAGRGVY 257
            GQTI EAL N+R MEA+GFRYSYDMLGEAA TA DAARY ADY  AIHAIG A+ GRG+Y
Sbjct: 195  GQTIAEALANSRRMEAKGFRYSYDMLGEAATTAADAARYLADYEGAIHAIGRAAQGRGIY 254

Query: 258  EGPGISIKLSAIHPRYSRAQADRVMDELLPRVKALALLAKGYDIGLNIDAEEADRLELSL 317
            EGPGISIKLSA+HPRYSRA+ +RVM ELLPRVK LALLAKGYDIGLNIDAEEADRLE+SL
Sbjct: 255  EGPGISIKLSALHPRYSRAKIERVMGELLPRVKGLALLAKGYDIGLNIDAEEADRLEISL 314

Query: 318  DLMESLCFDPDLAGWNGIGFVVQAYGKRCPYVIDFLIDLARRSGHRLMIRLVKGAYWDSE 377
            DL+E+L  DPDL+GWNGIGFV+QAYGKRCP+V+D+++DLARR+  R+M+RLVKGAYWDSE
Sbjct: 315  DLLEALALDPDLSGWNGIGFVIQAYGKRCPFVVDWIVDLARRANRRIMVRLVKGAYWDSE 374

Query: 378  IKRAQLDGLPDFPVYTRKVYTDVSYVACARKLLAAPEAVFPQFATHNAQTLATIYEMAGS 437
            IKRAQ DGL DFPV+TRKV+TDVSY+ACARKLLAAP+AVFPQFATHNAQTLA I  MAG 
Sbjct: 375  IKRAQTDGLEDFPVFTRKVHTDVSYLACARKLLAAPDAVFPQFATHNAQTLAAIMTMAGP 434

Query: 438  DFQVGKYEFQCLHGMGEPLYKEVVGP--LKRPCRIYAPVGTHETLLAYLVRRLLENGANS 495
            +F  G+YEFQCLHGMGEPLY+EVVGP  L RPCRIYAPVGTHETLLAYLVRRLLENGANS
Sbjct: 435  NFYRGQYEFQCLHGMGEPLYEEVVGPDKLNRPCRIYAPVGTHETLLAYLVRRLLENGANS 494

Query: 496  SFVNRIADPAVPVDELVADPVAVARAIAPTGAPHALIALPRNLYAPERANSAGIDLSDET 555
            SFVNRIAD  VP+ +L+ADPV V +A  P G PH  I LPR+L+ P+R NSAG+DLS+E 
Sbjct: 495  SFVNRIADEKVPIADLIADPVTVVQATNPAGEPHERITLPRHLFGPDRENSAGLDLSNEE 554

Query: 556  ELARLSAALSASAEMTWTAAPLLADGERAGQAQPVRNPADRRDVVGSVTEASEALVAEAF 615
             LA L+  L  S    W A P  +  +       VRNPADRRDVVG   EA+ A + EA 
Sbjct: 555  RLAALAEDLKRSVAQDWQALP--SKAKAPAPLTDVRNPADRRDVVGRWREATAAEMTEAL 612

Query: 616  GHAVAAASAWAATPPEERAASLFRAADTMQERMPTLLGLIVREAGKSLPNAIAEVREAID 675
              AV AA  WAATP  +RAA+L RAAD M+ RM  L+GLIVREAGKS PNA+AEVREA+D
Sbjct: 613  DAAVQAAPGWAATPAGDRAAALRRAADLMEARMGILIGLIVREAGKSFPNAVAEVREAVD 672

Query: 676  FLRYYGAQVRDRFDNATHRPLGPVVCISPWNFPLAIFSGQIAAALAAGNPVLAKPAEETP 735
            FLRYY A+V     +     LGPVVCISPWNFPLAIF+GQ+AAALAAGN VLAKPAEETP
Sbjct: 673  FLRYYAAEVVRTLGSDRLPALGPVVCISPWNFPLAIFTGQVAAALAAGNVVLAKPAEETP 732

Query: 736  LIAAEAVRILHAAGIPAGALQLLPGAGEVGAALVGHEAVRGVMFTGSTEVARLIQRQLAG 795
            LIAAEAVR+LH AGIP   LQL+PGAG VGAALV    V GVMFTGST VARLIQRQLA 
Sbjct: 733  LIAAEAVRLLHEAGIPIDGLQLVPGAGAVGAALVADPRVMGVMFTGSTAVARLIQRQLAD 792

Query: 796  RLLPDGAPIPLIAETGGQNAMIVDSSALAEQVVGDVIASAFDSAGQRCSALRILCLQEDV 855
            RL     PIP IAETGGQNA++VDSSALAEQVVGDVIASAFDSAGQRCSALRILCLQE+V
Sbjct: 793  RLTASDQPIPFIAETGGQNALVVDSSALAEQVVGDVIASAFDSAGQRCSALRILCLQEEV 852

Query: 856  ADRTLAMLKGAMRELRIGNPDRLAVDVGPVISEEARATIAAHIEAMRAKGRNVEFLPLPA 915
            ADR L ML+GAM EL +GNP  L+VDVGPVI+ EAR  I  H+  M A+G  V  LPL  
Sbjct: 853  ADRILEMLRGAMDELAVGNPGDLSVDVGPVITAEARDGIERHVTTMEARGHRVIRLPLGP 912

Query: 916  ETADGTFIAPTVIEIGGIHELEREVFGPVLHVVRFHRDDLDALVDSINATGYGLTFGLHT 975
            ET+ GTF+APT+IEIG I ++E+EVFGPVLHV+R+ R DLD L+D IN TGYGLTFGLHT
Sbjct: 913  ETSHGTFVAPTIIEIGRIADVEQEVFGPVLHVLRYRRADLDRLIDDINETGYGLTFGLHT 972

Query: 976  RIDATIERVTGRIGAGNVYVNRNTIGAVVGVQPFGGHGLSGTGPKAGGPLYLSRLLSRRP 1035
            RID TI RV  R+GAGNVYVNRN IGAVVGVQPFGG GLSGTGPKAGGPLYL RL+   P
Sbjct: 973  RIDETISRVVNRVGAGNVYVNRNIIGAVVGVQPFGGSGLSGTGPKAGGPLYLGRLMGTPP 1032

Query: 1036 KGWLEFRGPDAA---RAAGLAYGEWLRAKGFTAEASRCAGYVARSAIGGGAELNGPVGER 1092
            +  L  RG DAA    +    Y +WLRA+GF  +A R  G+V+RS++G   EL GPVGER
Sbjct: 1033 QTAL--RGLDAAPTTLSVARIYADWLRAQGFGEQAERVVGHVSRSSLGARVELPGPVGER 1090

Query: 1093 NLYELHGRGRVLLLPQTRTGLLLQLGAVLATGNSAAVDAPPDLAELLRGLPPALAARVRT 1152
            N+Y L  RGRV  L +T  GLL+Q+GA+LATGN A +DA   +  +L  LP  +   +  
Sbjct: 1091 NVYALRPRGRVAALAKTAEGLLVQVGAILATGNVAVLDAGSPVRAVLDHLPKEVRPSIEI 1150

Query: 1153 TADWRDVGPLAAVLVEGDRERVTAINRRVADLPGPILLVQAATAEALAAGRGEGYDLDLL 1212
              DWR    L  VL EGDR+ +  +NR VA   G I+ VQA TA AL    G+ YDL+ L
Sbjct: 1151 VPDWRATPELRGVLFEGDRDDLLQLNRAVAAREGSIVPVQATTAAALK--NGDDYDLNRL 1208

Query: 1213 LNERSVSVNTAAAGGNASLVAM 1234
            L E S+S NTAAAGGNASL+++
Sbjct: 1209 LEECSISTNTAAAGGNASLMSI 1230


Lambda     K      H
   0.319    0.136    0.396 

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: 3828
Number of extensions: 160
Number of successful extensions: 7
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: 1235
Length of database: 1231
Length adjustment: 47
Effective length of query: 1188
Effective length of database: 1184
Effective search space:  1406592
Effective search space used:  1406592
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.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources