Alignments for a candidate for put1 in Methyloferula stellata AR4T

GapMind for catabolism of small carbon sources

Alignments for a candidate for put1 in Methyloferula stellata AR4T

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_040580775.1 A3OQ_RS0108200 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

Query= reanno::psRCH2:GFF3021
         (1053 letters)



>NCBI__GCF_000385335.1:WP_040580775.1
          Length = 1025

 Score =  909 bits (2348), Expect = 0.0
 Identities = 516/1037 (49%), Positives = 658/1037 (63%), Gaps = 21/1037 (2%)

Query: 22   PAISANYSVDEAQYLTELLQLADPGEAGIAAIRERARSLIEAVRGRDNAVDTLDALLRQY 81
            P  +A Y+  +      LL   D   A +A +   A  L+ A+R +   +  L+  LR+Y
Sbjct: 2    PLFAAPYAEADEAIAPRLLAATDMDAAALARVDALASRLVSAIRSQSPRLGALEDFLREY 61

Query: 82   SLDTQEGLMLMCLAEALLRVPDAATADALIRDKLNAAEWERHLGQSDNVLVNFAAWGLVM 141
            SL T EGL LM LAEALLRVPD  TAD LI DKL  A + RH   SD +LV+ +AW L +
Sbjct: 62   SLSTDEGLALMVLAEALLRVPDDTTADRLIEDKLTHATFARHAAVSDALLVSASAWALGV 121

Query: 142  TGKVVDP-ETADGRPKNVIGRLLKRSGEPVIRGAMNQAMKLMGKQFVLGRTISEALKNGR 200
            T +++   ETA G    ++  L++R G   +R A  QAM+++G  F+LGR I E L +  
Sbjct: 122  TARMLQKGETAQG----IVASLVRRIGMSALRPAARQAMQILGAHFILGRNIEEGLAHSA 177

Query: 201  PEREKGYTYSFDMLGEAALTAEDAAKYMADYRQAVETVGAEPQVGKGP-RPSVSIKLSAL 259
                + Y YSFDMLGE A T+ DA  YM  YR A+ET+G E      P RP +S+KLSAL
Sbjct: 178  SGDGRLYRYSFDMLGEGARTSADAVHYMDAYRHAIETIGRESGTASLPQRPGISVKLSAL 237

Query: 260  HPRYELAQRERVLTELFGSVRELAILARRLNVGITIDAEEADRLELSLELYEKLLRDPAI 319
            HPR+EL  R RV+ EL   +  LA LA+  N+  T+DAEEADRLELSL+++  +L DPA+
Sbjct: 238  HPRFELLSRLRVMDELVPRLGSLARLAKDHNLSFTVDAEEADRLELSLDVFAAVLADPAL 297

Query: 320  AGWGEFGLVIQAYSKRCLPVLVWLTLLGRELGERIPLRLVKGAYWDSEIKQCQVQGLDGY 379
            AGW  FGL +QAY KR   VL ++  L R    R+ +RLVKGAYWD+EIK+ Q +GL  Y
Sbjct: 298  AGWDGFGLAVQAYQKRAGAVLDYVFDLARRHDRRLMVRLVKGAYWDTEIKRAQERGLTDY 357

Query: 380  PVYTRKEGTDTSYLACARYLLSEHTRGVIYPQFASHNAHTVSCILAMAEETAQPREFEFQ 439
            PV+TRK  TD +YL+CAR LL    RG I+PQFA+HNA TV+ I+   E       +EFQ
Sbjct: 358  PVFTRKPMTDLNYLSCARQLLD--ARGHIFPQFATHNALTVASIV---EYAGGVDGYEFQ 412

Query: 440  RLHGMGDALYDTV-IEKYARNVRIYAPVGAHKDLLPYLVRRLLENGANSSFVHQLVDPRV 498
            RLHGMG  L+  + ++      RIYAPVG ++DLL YLVRRLLENGANSSFV Q+ DP +
Sbjct: 413  RLHGMGADLFKALRLDFPDAACRIYAPVGTYRDLLAYLVRRLLENGANSSFVAQVGDPSI 472

Query: 499  PVESLIDHPVTQLRRFAAPGNPRIPLPPALFG-NRKNSQGINMNIQNQWTELASAYQPFL 557
            P++ L+ HP T +    A     +PLP  + G +RK+++G     + +   L  A     
Sbjct: 473  PLDILLRHPQTAI---GAGIFRALPLPEDIHGLSRKSARGFEFGARQELDALCKAVGEAP 529

Query: 558  ERQWQAAPVISGRTLAGTPSEVRCPYELNKVVGQAQFASADQARQAIDRLAAYWPIWNAT 617
                 A+ V  G T  G    V  P +   ++G+   +S D   +A+      + +W+A 
Sbjct: 530  GFYSVASIVAGGATQQGPSRPVLSPID-GSMIGEVGESSPDLIDRAMRAAQDAFKLWSAR 588

Query: 618  PVEARAAVLERLGDLLEQHRAELMALCTVEAGKSLQDGIDEVREAVDFCRYYAQQARLKL 677
            PVE RA  L+R+ D LE  R+  +AL   EAGK+L D + E+REAVDFCRYYA  AR   
Sbjct: 589  PVEERALCLDRMADGLEAERSRFLALLQSEAGKTLDDALGELREAVDFCRYYAACARHLF 648

Query: 678  GREE-LKGPTGERNELFHEGRGVFVCVSPWNFPLAIYLGQITAALVAGNTVLAKPAEQTS 736
               E + GPTGE N L H GRG F+C+SPWNFPL+I+LGQ+ AALVAGN V+AKPAEQT 
Sbjct: 649  STSEIMPGPTGEENRLTHFGRGTFICISPWNFPLSIFLGQVAAALVAGNAVIAKPAEQTP 708

Query: 737  LIAARALELMFEAGLPQEAIAFLPGDGATLGGVFCRDPRVVGVCFTGSTDTARIINRQLA 796
            LIA+ A  L+    +P   +  LPGDG+T G      P + GV FTGST+TA  INR LA
Sbjct: 709  LIASEAALLLHRCSVPGAVLQLLPGDGST-GAALVASPHIAGVVFTGSTETAFAINRALA 767

Query: 797  EKEGPIATLIAETGGQNAMIVDSTALPEQVIKDAVGSAFTSAGQRCSALRVLYVQRDIAD 856
             K+GPI   IAETGG NAMIVD+TALPEQV  D + SAF SAGQRCSALR+L VQ D+AD
Sbjct: 768  AKDGPIVPFIAETGGINAMIVDATALPEQVTDDVIASAFRSAGQRCSALRLLCVQEDVAD 827

Query: 857  RVIDLLKGAMAELRVGPTHLRENDIGPVIDQEAREGLLAHIQQLKSEGRLIAEATVPAG- 915
            RVI ++ GA AEL VG        +GPVID  AR+ L  HI  +K   R+    +VPAG 
Sbjct: 828  RVITMIAGAAAELVVGDPRDLSTHVGPVIDAAARDALETHIAAMKQSARVHFAGSVPAGA 887

Query: 916  -LNGHFVAPVAFEIDGIHQLKKEHFGPVLHVVRYDAADLEKVVAAINGTGYGLTLGVHSR 974
               G +VAP  FE+  + +L++E FGPVLHVVRY AA+L+ ++ AI   GYGLTLG+HSR
Sbjct: 888  PARGFYVAPHIFELASVAELEREVFGPVLHVVRYKAAELDALLDAIAAKGYGLTLGIHSR 947

Query: 975  NEETAERIEQLARVGNLYVNRNQIGAVVGVQPFGGCRLSGTGPKAGGPSYLLRFANERTT 1034
             + T E I      GN+YVNR+ IGAVVG QPFGG  LSGTGPKAGGP+YL RF  E T 
Sbjct: 948  IDATIEHIIARRLAGNVYVNRSMIGAVVGTQPFGGFGLSGTGPKAGGPNYLKRFMLEETV 1007

Query: 1035 STNTTAVGGNASLLSLG 1051
            S NT AVGGNASL+S G
Sbjct: 1008 SINTAAVGGNASLMSQG 1024


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: 2392
Number of extensions: 115
Number of successful extensions: 10
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: 1053
Length of database: 1025
Length adjustment: 45
Effective length of query: 1008
Effective length of database: 980
Effective search space:   987840
Effective search space used:   987840
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: 57 (26.6 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