Alignments for a candidate for put1 in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for put1 in Sinorhizobium meliloti 1021

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate SMc02181 SMc02181 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase

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



>FitnessBrowser__Smeli:SMc02181
          Length = 1233

 Score = 1637 bits (4239), Expect = 0.0
 Identities = 860/1227 (70%), Positives = 964/1227 (78%), Gaps = 9/1227 (0%)

Query: 10   AAPGEAAPFADFAPPIRPATELRAAITAAYRRPEPECLPFLFEQASLPPGVITAAAATAR 69
            AAP   APFADFAPP+RP + LR AITAAYRRPE ECLP L E A+    +  AAA+TAR
Sbjct: 13   AAP---APFADFAPPVRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTAR 69

Query: 70   KLITALRAKPRGRGVEGLIHEYSLSSQEGMALMCLAEALLRIPDHATRDALIRDKIAGGD 129
            KLI ALR K  G GVEGL+ EYSLSSQEG+ALMCLAEALLRIPD ATRDALIRDKIA G+
Sbjct: 70   KLIEALRGKHSGSGVEGLVQEYSLSSQEGVALMCLAEALLRIPDTATRDALIRDKIADGN 129

Query: 130  WQAHLGKGGSMFVNAATWGLLITGKLTSAGGEQALSSALTRLIARGGEPLIRRGVDFAMR 189
            W++HLG   S+FVNAATWGL++TGKLTS   +++L++ALTRLI+R GEP+IRRGVD AMR
Sbjct: 130  WKSHLGGSRSLFVNAATWGLVVTGKLTSTVNDRSLAAALTRLISRCGEPVIRRGVDMAMR 189

Query: 190  MMGEQFVTGQTIQEALTNARTMEAEGFRYSYDMLGEAALTAEDAARYYADYVNAIHAIGT 249
            MMGEQFVTG+TI+EAL  ++ +E +GF YSYDMLGEAA TA DA RYY DY +AIHAIG 
Sbjct: 190  MMGEQFVTGETIREALKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGK 249

Query: 250  ASAGRGVYEGPGISIKLSAIHPRYSRAQADRVMDELLPRVKALALLAKGYDIGLNIDAEE 309
            ASAGRG+YEGPGISIKLSA+HPRYSRAQA RVM ELLPRVKALALLAK YDIGLNIDAEE
Sbjct: 250  ASAGRGIYEGPGISIKLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEE 309

Query: 310  ADRLELSLDLMESLCFDPDLAGWNGIGFVVQAYGKRCPYVIDFLIDLARRSGHRLMIRLV 369
            ADRLELSLDL+E LC D DL+GWNG+GFVVQAYGKRCP+V+DF+IDLARRSG R+M+RLV
Sbjct: 310  ADRLELSLDLLEVLCLDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLV 369

Query: 370  KGAYWDSEIKRAQLDGLPDFPVYTRKVYTDVSYVACARKLLAAPEAVFPQFATHNAQTLA 429
            KGAYWD+EIKRAQLDGL DFPV+TRK++TDVSY+ACA KLLAA + VFPQFATHNAQTLA
Sbjct: 370  KGAYWDAEIKRAQLDGLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLA 429

Query: 430  TIYEMAGSDFQVGKYEFQCLHGMGEPLYKEVV--GPLKRPCRIYAPVGTHETLLAYLVRR 487
             IY MAG DF VGKYEFQCLHGMGEPLY+EVV  G L RPCRIYAPVGTHETLLAYLVRR
Sbjct: 430  AIYHMAGKDFHVGKYEFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRR 489

Query: 488  LLENGANSSFVNRIADPAVPVDELVADPVAVARAIAPTGAPHALIALPRNLYAPERANSA 547
            LLENGANSSFV+RI DP V +DEL+ADPV V RA+   GA H  IALP  L+   R NSA
Sbjct: 490  LLENGANSSFVHRINDPKVSIDELIADPVEVVRAMPVVGAKHDRIALPAELFGDARTNSA 549

Query: 548  GIDLSDETELARLSAALSASAEMTWTAAPLLADGERAGQAQPVRNPADRRDVVGSVTEAS 607
            G+DLS+E  LA L+ AL  SA M WTA P LA G  AG+ + V NP D RDVVGSVTE S
Sbjct: 550  GLDLSNEETLASLTEALRESAAMKWTALPQLATGPAAGETRTVLNPGDHRDVVGSVTETS 609

Query: 608  EALVAEAFGHAVAAASAWAATPPEERAASLFRAADTMQERMPTLLGLIVREAGKSLPNAI 667
            E     A   A  AA  WAA PP ERAA L RAA+ MQ RMPTLLGLI+REAGKS  NAI
Sbjct: 610  EEDARRAVRLAADAAPDWAAVPPSERAACLDRAAELMQARMPTLLGLIIREAGKSALNAI 669

Query: 668  AEVREAIDFLRYYGAQVRDRFDNATHRPLGPVVCISPWNFPLAIFSGQIAAALAAGNPVL 727
            AEVREAIDFLRYY  Q R R     H PLGP+VCISPWNFPLAIF+GQIAAAL AGNPVL
Sbjct: 670  AEVREAIDFLRYYAEQTR-RTLGPGHGPLGPIVCISPWNFPLAIFTGQIAAALVAGNPVL 728

Query: 728  AKPAEETPLIAAEAVRILHAAGIPAGALQLLPGAGEVGAALVGHEAVRGVMFTGSTEVAR 787
            AKPAEETPLIAAE VRIL  AGIPA ALQLLPG G VGAALV      GVMFTGSTEVAR
Sbjct: 729  AKPAEETPLIAAEGVRILREAGIPASALQLLPGDGRVGAALVAAAETAGVMFTGSTEVAR 788

Query: 788  LIQRQLAGRLLPDGAPIPLIAETGGQNAMIVDSSALAEQVVGDVIASAFDSAGQRCSALR 847
            LIQ QLA RL P G PIPLIAETGGQNAMIVDSSALAEQVVGDVI SAFDSAGQRCSALR
Sbjct: 789  LIQAQLADRLSPAGRPIPLIAETGGQNAMIVDSSALAEQVVGDVITSAFDSAGQRCSALR 848

Query: 848  ILCLQEDVADRTLAMLKGAMRELRIGNPDRLAVDVGPVISEEARATIAAHIEAMRAKGRN 907
            +LCLQEDVADR L MLKGA+ EL IG  DRL+VDVGPVI+ EA+  I  HIE MR  GR 
Sbjct: 849  VLCLQEDVADRILTMLKGALHELHIGRTDRLSVDVGPVITSEAKDNIEKHIERMRGLGRK 908

Query: 908  VEFLPLPAETADGTFIAPTVIEIGGIHELEREVFGPVLHVVRFHRDDLDALVDSINATGY 967
            VE + L +ET  GTF+ PT+IE+  + +L+REVFGPVLHV+R+ RDDLD LVD +NATGY
Sbjct: 909  VEQIGLASETGVGTFVPPTIIELEKLSDLQREVFGPVLHVIRYRRDDLDRLVDDVNATGY 968

Query: 968  GLTFGLHTRIDATIERVTGRIGAGNVYVNRNTIGAVVGVQPFGGHGLSGTGPKAGGPLYL 1027
            GLTFGLHTR+D TI  VT RI AGN+Y+NRN IGAVVGVQPFGG GLSGTGPKAGGPLYL
Sbjct: 969  GLTFGLHTRLDETIAHVTSRIKAGNLYINRNIIGAVVGVQPFGGRGLSGTGPKAGGPLYL 1028

Query: 1028 SRLLSRRPKGWLEFRGPDAARAAGLAYGEWLRAKGFTAEASRCAGYVARSAIGGGAELNG 1087
             RL++  P                L + +WL  KG  AEA       + SA+G   EL G
Sbjct: 1029 GRLVTTAPVP--PQHSSVHTDPVLLDFAKWLDGKGARAEAEAARNAGSSSALGLDLELPG 1086

Query: 1088 PVGERNLYELHGRGRVLLLPQTRTGLLLQLGAVLATGNSAAVDAPPDLAELLRGLPPALA 1147
            PVGERNLY LH RGR+LL+P T +GL  QL A LATGNS A+DA   L   L+ LP  + 
Sbjct: 1087 PVGERNLYTLHARGRILLVPATESGLYHQLAAALATGNSVAIDAASGLQASLKNLPQTVG 1146

Query: 1148 ARVRTTADWRDVGPLAAVLVEGDRERVTAINRRVADLPGPILLVQAATAEALAAGRGEGY 1207
             RV  + DW   GP A  LVEGD ER+ A+N+ +A LPGP+LLVQAA++  +A    + Y
Sbjct: 1147 LRVSWSKDWAADGPFAGALVEGDAERIRAVNKAIAALPGPLLLVQAASSGEIAR-NPDAY 1205

Query: 1208 DLDLLLNERSVSVNTAAAGGNASLVAM 1234
             L+ L+ E S S+NTAAAGGNASL+A+
Sbjct: 1206 CLNWLVEEVSASINTAAAGGNASLMAI 1232


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: 3806
Number of extensions: 156
Number of successful extensions: 6
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: 1233
Length adjustment: 48
Effective length of query: 1187
Effective length of database: 1185
Effective search space:  1406595
Effective search space used:  1406595
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 Apr 09 2024. 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 2024 update 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