Alignments for a candidate for put1 in Azospirillum lipoferum B510

GapMind for catabolism of small carbon sources

Alignments for a candidate for put1 in Azospirillum lipoferum B510

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_012978279.1 AZL_RS30800 trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase

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



>NCBI__GCF_000010725.1:WP_012978279.1
          Length = 1244

 Score = 1806 bits (4678), Expect = 0.0
 Identities = 942/1232 (76%), Positives = 1026/1232 (83%), Gaps = 20/1232 (1%)

Query: 17   PFADFAPPIRPATELRAAITAAYRRPEPECLPFLFEQASLPPGVITAAAATARKLITALR 76
            PFA FAP +RPA+ LR AITAAYRRPEP+C+ +L EQA+LP  V  AAA TAR LI ALR
Sbjct: 20   PFAAFAPVVRPASPLRQAITAAYRRPEPDCVAWLVEQAALPAEVTAAAARTARSLIAALR 79

Query: 77   AKPRGRGVEGLIHEYSLSSQEGMALMCLAEALLRIPDHATRDALIRDKIAGGDWQAHLGK 136
            A+P+GRGVEGLIHEYSLSSQEG+ALMCLAEALLRIPD ATRDALIRDKIAGGDW+AHLG 
Sbjct: 80   ARPQGRGVEGLIHEYSLSSQEGVALMCLAEALLRIPDRATRDALIRDKIAGGDWRAHLGN 139

Query: 137  GGSMFVNAATWGLLITGKLTSA-----GGEQALSSALTRLIARGGEPLIRRGVDFAMRMM 191
              S+FVNAATWGLL+TGK+T       GGEQALSSALT+LI RGGEPLIRRGVDFAMRMM
Sbjct: 140  SPSLFVNAATWGLLVTGKVTGVLGDHFGGEQALSSALTKLILRGGEPLIRRGVDFAMRMM 199

Query: 192  GEQFVTGQTIQEALTNARTMEAEGFRYSYDMLGEAALTAEDAARYYADYVNAIHAIGTAS 251
            GEQFVTGQTI EAL N+R MEAEGFRYSYDMLGEAA TA DA RYYADY  AIHAIG AS
Sbjct: 200  GEQFVTGQTIDEALANSRGMEAEGFRYSYDMLGEAATTAADADRYYADYEKAIHAIGKAS 259

Query: 252  AGRGVYEGPGISIKLSAIHPRYSRAQADRVMDELLPRVKALALLAKGYDIGLNIDAEEAD 311
            AGRG+++GPGISIKLSA+HPRYSRAQ  RVM ELLPRV  LA LA+ YDIGLNIDAEEAD
Sbjct: 260  AGRGIHDGPGISIKLSALHPRYSRAQGQRVMAELLPRVTELARLARRYDIGLNIDAEEAD 319

Query: 312  RLELSLDLMESLCFDPDLAGWNGIGFVVQAYGKRCPYVIDFLIDLARRSGHRLMIRLVKG 371
            RLELSLDL+ESLCFDPDLAGWNGIGFVVQAYGKRCPYVIDF++DLARRSGHRLMIRLVKG
Sbjct: 320  RLELSLDLLESLCFDPDLAGWNGIGFVVQAYGKRCPYVIDFVVDLARRSGHRLMIRLVKG 379

Query: 372  AYWDSEIKRAQLDGLPDFPVYTRKVYTDVSYVACARKLLAAPEAVFPQFATHNAQTLATI 431
            AYWDSEIKRAQ+DGL DFPVYTRK++TDVSYVACAR+LL AP+AVFPQFATHNAQTLATI
Sbjct: 380  AYWDSEIKRAQVDGLEDFPVYTRKLHTDVSYVACARRLLGAPDAVFPQFATHNAQTLATI 439

Query: 432  YEMAG----SDFQVGKYEFQCLHGMGEPLYKEVVGPLKRPCRIYAPVGTHETLLAYLVRR 487
            + MA     + FQVG+YEFQCLHGMGEPLYKEVVGPLKRPCR+YAPVGTHETLLAYLVRR
Sbjct: 440  HRMAEHLNPAGFQVGQYEFQCLHGMGEPLYKEVVGPLKRPCRVYAPVGTHETLLAYLVRR 499

Query: 488  LLENGANSSFVNRIADPAVPVDELVADPVAVARAIAPTGAPHALIALPRNLYAPERANSA 547
            LLENGANSSFVNRIAD +V +D+LVADPVA A A  P G  + LIALP++L+  ERANSA
Sbjct: 500  LLENGANSSFVNRIADKSVSIDDLVADPVAQASATLPLGERNPLIALPKDLFGAERANSA 559

Query: 548  GIDLSDETELARLSAALSASAEMTWTAAPLLADGERAGQ----AQPVRNPADRRDVVGSV 603
            G+DLS+ET LA LSAAL  SA + WTAAPLLADGER G+    A+PV NPADRRD+VG  
Sbjct: 560  GLDLSNETTLAGLSAALRDSAAIAWTAAPLLADGERRGEHPGKARPVLNPADRRDIVGRR 619

Query: 604  TEASEALVAEAFGHAVAAASAWAATPPEERAASLFRAADTMQERMPTLLGLIVREAGKSL 663
             +A  A +A+AF  A AAA  WAATPP ERAA LFRAAD MQ R+PTLLGLI+REAGKS 
Sbjct: 620  VDAGPADIADAFLFAEAAAPVWAATPPAERAACLFRAADAMQARLPTLLGLIIREAGKST 679

Query: 664  PNAIAEVREAIDFLRYYGAQVRDRFDNATHRPLGPVVCISPWNFPLAIFSGQIAAALAAG 723
             NAIAE+REAIDFLRYYGAQVRDRF N TH PLGPVVCISPWNFPLAIF+GQ+AAALAAG
Sbjct: 680  ANAIAELREAIDFLRYYGAQVRDRFANDTHLPLGPVVCISPWNFPLAIFTGQVAAALAAG 739

Query: 724  NPVLAKPAEETPLIAAEAVRILHAAGIPAGALQLLPGAGEVGAALVGHEAVRGVMFTGST 783
            NPVLAKPAEETPL+A EAVRIL AAG+PAGA+QLLPGAGEVGAALVGH   R VMFTGST
Sbjct: 740  NPVLAKPAEETPLVATEAVRILRAAGVPAGAVQLLPGAGEVGAALVGHAGTRAVMFTGST 799

Query: 784  EVARLIQRQLAGRLLPDGAPIPLIAETGGQNAMIVDSSALAEQVVGDVIASAFDSAGQRC 843
            EVARLIQRQLA RL PDGAPIPLIAETGGQNAMIVDSSALAEQVV DVIASAFDSAGQRC
Sbjct: 800  EVARLIQRQLAERLSPDGAPIPLIAETGGQNAMIVDSSALAEQVVADVIASAFDSAGQRC 859

Query: 844  SALRILCLQEDVADRTLAMLKGAMRELRIGNPDRLAVDVGPVISEEARATIAAHIEAMRA 903
            SALRILCLQEDVADRTL MLKGAMREL IG+PDRLAVDVGPVI+ EAR  I  HIEAMRA
Sbjct: 860  SALRILCLQEDVADRTLTMLKGAMRELGIGSPDRLAVDVGPVITAEARDGILRHIEAMRA 919

Query: 904  KGRNVEFLPLPAETADGTFIAPTVIEIGGIHELEREVFGPVLHVVRFHRDDLDALVDSIN 963
            KGR VE LPLPAET  GTF+APT+IEI  I +LEREVFGPVLHV+RF RDDLD LVD+IN
Sbjct: 920  KGRRVESLPLPAETGHGTFVAPTIIEIDRIADLEREVFGPVLHVLRFRRDDLDRLVDAIN 979

Query: 964  ATGYGLTFGLHTRIDATIERVTGRIGAGNVYVNRNTIGAVVGVQPFGGHGLSGTGPKAGG 1023
             TGYGLTFGLHTRIDATI+RVT RI AGN+YVNRNTIGAVVGVQPFGGHGLSGTGPKAGG
Sbjct: 980  GTGYGLTFGLHTRIDATIDRVTSRIEAGNLYVNRNTIGAVVGVQPFGGHGLSGTGPKAGG 1039

Query: 1024 PLYLSRLLSRRPKGWLEFRGPDAARAAGLAYGEWLRAKGFTAEASRCAGYVARSAIGGGA 1083
            PLYLSRLLS RP   L  RG    RA    +  WL  +G  A A+        S +GG  
Sbjct: 1040 PLYLSRLLSVRPLPDLGVRG-GTERALAHNFAGWLADQGKAAIATEVRALAKHSPVGGRT 1098

Query: 1084 ELNGPVGERNLYELHGRGRVLLLPQTRTGLLLQLGAVLATGNSAAVDAPPDLAELLRGLP 1143
            EL GPVGE N+Y L  RGR+LLLP+T  GL   LGA LATGN   VD    +   L  LP
Sbjct: 1099 ELAGPVGESNVYSLMPRGRILLLPRTEDGLYRLLGAALATGNEVVVDGDTAVTAGLTRLP 1158

Query: 1144 PALAARVRTTADWRDVGPLAAVLVEGDRERVTAINRRVADLPGPILLVQAATAEALAAGR 1203
            P +AARVR +  W   GPLA  LVEG+ ER+ A NRR+A+LPGPI+L Q           
Sbjct: 1159 PEVAARVRVSPSWTSFGPLAGALVEGESERLLAANRRIAELPGPIVLTQGVPT------G 1212

Query: 1204 GEGYDLDLLLNERSVSVNTAAAGGNASLVAMS 1235
            G+G ++  L+NERSVS NT AAGGNASLVAMS
Sbjct: 1213 GKGVEIAWLMNERSVSTNTTAAGGNASLVAMS 1244


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: 4231
Number of extensions: 211
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: 1244
Length adjustment: 48
Effective length of query: 1187
Effective length of database: 1196
Effective search space:  1419652
Effective search space used:  1419652
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