Alignments for a candidate for put1 in Azorhizobium caulinodans ORS 571

GapMind for catabolism of small carbon sources

Alignments for a candidate for put1 in Azorhizobium caulinodans ORS 571

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_043878684.1 AZC_RS00160 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

Query= reanno::SB2B:6938573
         (1058 letters)



>NCBI__GCF_000010525.1:WP_043878684.1
          Length = 1041

 Score =  932 bits (2409), Expect = 0.0
 Identities = 504/1027 (49%), Positives = 672/1027 (65%), Gaps = 13/1027 (1%)

Query: 31   DEEAYLKELIALVPSSDEEIARITSRAHDLVAKVRQYEKKGLMVGIDAFLQQYSLETQEG 90
            D+ A  + L+A    + E  ARI + A  L+  +R+    G + GI+  L++Y+L T+EG
Sbjct: 27   DDVALARPLLAQGTLAPEAEARIDALAARLITAIRKGSNAGGVGGIEEVLREYALSTKEG 86

Query: 91   IILMCLAEALLRIPDAETADALIADKLSGAKWDEHMSKSDSVLVNASTWGLMLTGKIVQL 150
            + LM LAEALLR+PD+ TAD LI DKL+   +  H S+S ++LVNAS+W L +T +++Q 
Sbjct: 87   LALMTLAEALLRVPDSATADRLIEDKLAQGDFLNHDSRSSALLVNASSWALGVTARVIQP 146

Query: 151  DKNLDGTPSNLLSRLVNRLGEPVIRQAMYAAMKIMGKQFVLGRTIEEGLKNAAEKRKLGY 210
             +    TP  +L +L  R+G P +R A   AMK++G  FVLG+TI   L  A       Y
Sbjct: 147  GE----TPEGVLGKLAKRIGLPAVRTATRQAMKVLGNHFVLGQTIHAALDRAESASGRAY 202

Query: 211  THSYDMLGEAALTMKDADKYYRDYANAIQALGTAKFDESEAPRPTISIKLSALHPRYEVA 270
             +S+DMLGE A T  DA +Y+  YA AI  +G    +     RP IS+KLSALHPRY+  
Sbjct: 203  RYSFDMLGEGARTFTDAKRYFDSYATAIDDIGRRAGNMKLPDRPGISVKLSALHPRYDAV 262

Query: 271  NEDRVMTELYATLIKLIEQARSLNVGIQIDAEEVDRLELSLKLFKKLYQSDAAKGWGLLG 330
            N +RV+ EL   +I+L  +A++ ++   IDAEE DRLELSL +   +       GW   G
Sbjct: 263  NRERVLIELVPQVIELARKAKAYDLNFTIDAEEADRLELSLDVIDAVLADPGLAGWDGFG 322

Query: 331  IVVQAYSKRALPVLMWLTRLAKEQGDEIPLRLVKGAYWDSELKWAQQAGEAGYPLFTRKA 390
            + +QAY KRA  V+  +  LA+     + LRLVKGAYWD+E+K AQ+ G   YP+FTRKA
Sbjct: 323  LAIQAYQKRAAAVIDHMAALAERLDRRLMLRLVKGAYWDTEVKRAQERGLDDYPVFTRKA 382

Query: 391  ATDVSYLACARYLLSEATRGVIYPQFASHNAQTVAAITAMVGDR-KFEFQRLHGMGQELY 449
             TD++Y+ACAR LL  A R  I+PQFA+HNA T+A IT + G    FEFQRLHGMG   +
Sbjct: 383  MTDLNYMACARKLL--ALRPRIFPQFATHNALTIATITELSGGTGGFEFQRLHGMGDAAH 440

Query: 450  DTVLAEAAVPTVRIYAPIGAHKDLLPYLVRRLLENGANTSFVHKLVDPKTPIESLVTHPL 509
               LA       R YAP+G H+DLL YLVRRLLENGAN+SFV    DP  P+  L+  P 
Sbjct: 441  GERLAAHPDVGCRTYAPVGGHRDLLAYLVRRLLENGANSSFVSVAGDPDVPVSDLLRRPA 500

Query: 510  KTLQGYKTLANNKIVKPADIFGAERKNSKGLNMNIISESEPFFAALEKFKDTQWSAGPLV 569
              +   +   N  I  P D+FG  R+NS G+ +   S        +   +  + +A  L+
Sbjct: 501  TLIGNAEEARNRHIPLPPDLFGPGRRNSHGVELGCRSVLAATLTDIAGHR-REVTASTLI 559

Query: 570  NGETLSGEVRDVVSPYNTTLKVGQVAFANEATIEQAIAGADKAFASWCRTPVETRANALQ 629
            +G   +G  R VVSP + +  +G+V  A+ AT + A+A A K F +W RTP   R+  L+
Sbjct: 560  DGVAHAGATRTVVSPIDGS-AIGRVVEADAATADAAVAAALKGFVAWDRTPASERSARLR 618

Query: 630  KLADLLEENREELIALCTREAGKSIQDGIDEVREAVDFCRYYAVQAKKMMSKPELLPGPT 689
            + ADLLE  +   +AL   EAGK++ DGI EVREAVDF RYYA +A+++    E LPGPT
Sbjct: 619  RAADLLEARQAAFLALLQDEAGKTLDDGISEVREAVDFLRYYAGEAERLCGAGETLPGPT 678

Query: 690  GELNELFLQGRGVFVCISPWNFPLAIFLGQVAAALATGNTVIAKPAEQTCLIGFRAVQLA 749
            GE N L L+GRGVFV ISPWNFPLAIFLGQV+AALA GN V+AKPAEQT LI F AV+L 
Sbjct: 679  GESNVLRLRGRGVFVAISPWNFPLAIFLGQVSAALAAGNAVVAKPAEQTPLIAFEAVRLL 738

Query: 750  HEAGIPKDVLQFLPGTGAVVGAKLTSDERIGGVCFTGSTTTAKVINRALAGRDGAIIPLI 809
            HEAG+P   L  + G G ++GA+L    ++ GV FTGST  A++INR LAG+DG I+PLI
Sbjct: 739  HEAGVPASALHLVTGDG-LIGARLVEAPKVAGVVFTGSTEVARIINRTLAGKDGPIVPLI 797

Query: 810  AETGGQNAMVVDSTSQPEQVVNDVVSSAFTSAGQRCSALRVLYLQEDIAERVLDVLKGAM 869
            AETGG NAM+VD+T+ PEQV +DVV+SAF SAGQRCSALR+L++QED+A+++++++ GA 
Sbjct: 798  AETGGINAMIVDATALPEQVSDDVVTSAFRSAGQRCSALRILFVQEDVADKMIEMIVGAA 857

Query: 870  DELTLGNPGSVKTDVGPVIDAAAKANLNAHIDHIKQVGRLIHQLSLPEGTENGHFVAPTA 929
            D L +G+P      VGPVIDA AKA L AHI  +    R+ +  + P     G +VAP  
Sbjct: 858  DALKVGDPRDASVHVGPVIDAEAKAKLEAHIRALTGTARVHYAGTAP---TRGTYVAPHV 914

Query: 930  VEIDSIKVLTKENFGPILHVVRYKAAGLQKVIDDINSTGFGLTLGIHSRNEGHALEVADK 989
             E+     L  E FGP+LHVVR+KA G+  V+D I +TG+GLTLG+H+R +    +V ++
Sbjct: 915  FELKQAADLKDEVFGPVLHVVRFKAGGIDGVLDAIAATGYGLTLGLHTRIDSLVEKVTER 974

Query: 990  VNVGNVYINRNQIGAVVGVQPFGGQGLSGTGPKAGGPHYLTRFVTEKTRTNNITAIGGNA 1049
            + VGNVY+NRN IGAVVGVQPFGG GLSGTGPKAGGPHYL RF +E+T T N +A GGNA
Sbjct: 975  LPVGNVYVNRNIIGAVVGVQPFGGHGLSGTGPKAGGPHYLLRFASEQTVTINTSAAGGNA 1034

Query: 1050 TLLSLGD 1056
             L++ G+
Sbjct: 1035 ALMTQGE 1041


Lambda     K      H
   0.317    0.134    0.380 

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: 2493
Number of extensions: 114
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: 1058
Length of database: 1041
Length adjustment: 45
Effective length of query: 1013
Effective length of database: 996
Effective search space:  1008948
Effective search space used:  1008948
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: 58 (26.9 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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