Alignments for a candidate for put1 in Methylocystis bryophila S285

GapMind for catabolism of small carbon sources

Alignments for a candidate for put1 in Methylocystis bryophila S285

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_085770261.1 B1812_RS02885 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

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



>NCBI__GCF_002117405.1:WP_085770261.1
          Length = 1018

 Score =  846 bits (2185), Expect = 0.0
 Identities = 484/1026 (47%), Positives = 641/1026 (62%), Gaps = 28/1026 (2%)

Query: 28   YIVDEEAYLKELIALVPSSDEEIARITSRAHDLVAKVRQYEKKGLMVG-IDAFLQQYSLE 86
            Y  D+      L+A  P      A   + A +LVA  R    +GL++G I+ FL+++SL 
Sbjct: 14   YAEDDAQIAARLLARRPDPGARDAT-EALARELVAASRP---QGLLIGGIEDFLREFSLT 69

Query: 87   TQEGIILMCLAEALLRIPDAETADALIADKLSGAKWDEHMSKSDSVLVNASTWGLMLTGK 146
            ++EG+ +M LAE+LLR+PD ET D L+ADKL+   +  H    D++LV A  + L L+ +
Sbjct: 70   SREGLAVMALAESLLRVPDDETLDRLLADKLAVGDFAHHRIAGDALLVQACAFALGLSAR 129

Query: 147  IVQLDKNLDGTPSNLLSRLVNRLGEPVIRQAMYAAMKIMGKQFVLGRTIEEGLKNAAEKR 206
            + +       +P      +  RLG P +R A   AM++MG  FV G TIE    NA  +R
Sbjct: 130  LFEEG----ASPHGAAESVARRLGLPALRLAAKQAMRLMGAHFVFGETIE----NALSRR 181

Query: 207  KLGYTHSYDMLGEAALTMKDADKYYRDYANAIQALGTAKFDESEAPRPTISIKLSALHPR 266
                 +S+DMLGEAA T +DA++Y+  YA+AI+A+G A   ++   RP +S+KLSALHPR
Sbjct: 182  APHLRYSFDMLGEAARTQEDAERYFEAYAHAIEAVGGAAGAQALPERPGVSVKLSALHPR 241

Query: 267  YEVANEDRVMTELYATLIKLIEQARSLNVGIQIDAEEVDRLELSLKLFKKLYQSDAAKGW 326
            YE  + +RV+ EL   L+ L   AR  ++   IDAEE DRLELSL +  ++    + KGW
Sbjct: 242  YEAISRERVLAELAPRLLDLARLAREHDLAFTIDAEEADRLELSLDVMARVVADPSLKGW 301

Query: 327  GLLGIVVQAYSKRALPVLMWLTRLAKEQGDEIPLRLVKGAYWDSELKWAQQAGEAGYPLF 386
               G+ VQAY KRA  V+  +   AK     + LRLVKGAYWD E+K AQ+ G A YP+F
Sbjct: 302  EGFGLAVQAYQKRAEAVIDHVAGWAKTLNRRLMLRLVKGAYWDLEIKRAQERGLADYPVF 361

Query: 387  TRKAATDVSYLACARYLLSEATRGVIYPQFASHNAQTVAAITAM-VGDRKFEFQRLHGMG 445
            TRKA TD +YLACA  L +E    +++PQFA+HNA T AAI A       FEFQRLHGMG
Sbjct: 362  TRKAMTDANYLACAARLFAEP---MLFPQFATHNAMTAAAILAQGAKPESFEFQRLHGMG 418

Query: 446  QELYDTVLAEAAVPTVRIYAPIGAHKDLLPYLVRRLLENGANTSFVHKLVDPKTPIESLV 505
            + LY  +L + A   VR+YAP+G H+DLL YLVRRL+ENGAN+S+V +L DP   IE L+
Sbjct: 419  EGLYGLLLQKGA--AVRVYAPVGKHRDLLAYLVRRLIENGANSSYVARLADPHCGIEDLL 476

Query: 506  THPLKTLQGYKTLANNKIVKPADIFGAERKNSKGLNMNIISESEPFFAALEKFKDTQWSA 565
              P   L   +   +  +  P D++   R NS G+              ++  +  ++ A
Sbjct: 477  EDPFAALGRPENARHRHLPLPKDLYRPLRSNSDGVEFGDQKALSALLVEIDASRGAKFFA 536

Query: 566  GPLVNGETLSGEVRDVVSPYNTTLKVGQVAFANEATIEQAIAGADKAFASWCRTPVETRA 625
             P     T   + R + SP++ T +VG V  A+ A+++ A+A A +AF++W   P ETRA
Sbjct: 537  QPASASMT---QKRAIHSPFDGT-RVGDVIEADAASLDVAMAAAHRAFSAWGAQPAETRA 592

Query: 626  NALQKLADLLEENREELIALCTREAGKSIQDGIDEVREAVDFCRYYAVQAKKMMSKPELL 685
              L++ A L+E  R  LIAL   E GK++ D + EVREA D+CRYYA  A+++M +   L
Sbjct: 593  QILERAAALIESRRGRLIALLQSEGGKTLDDALAEVREAADYCRYYANVARELM-RERAL 651

Query: 686  PGPTGELNELFLQGRGVFVCISPWNFPLAIFLGQVAAALATGNTVIAKPAEQTCLIGFRA 745
            PGPTGE N L   GRGVFVCISPWNFPLAIF+GQ+AAAL  GN V AKPAEQT LIGF A
Sbjct: 652  PGPTGEENRLRHVGRGVFVCISPWNFPLAIFVGQIAAALVAGNAVAAKPAEQTPLIGFEA 711

Query: 746  VQLAHEAGIPKDVLQFLPGTGAVVGAKLTSDERIGGVCFTGSTTTAKVINRALAGRDGAI 805
            V L  EAG+P D LQFLPG GA VGA L + E   GV FTGS   A+ INRALA + G I
Sbjct: 712  VALLREAGVPADALQFLPGDGA-VGASLVAHELTAGVVFTGSVAVAQEINRALAKKPGPI 770

Query: 806  IPLIAETGGQNAMVVDSTSQPEQVVNDVVSSAFTSAGQRCSALRVLYLQEDIAERVLDVL 865
            +PLIAETGG NAM+VDST+  E V +DV +SAF SAGQRCSALR+LYLQE+I +  L  +
Sbjct: 771  VPLIAETGGINAMIVDSTALFEHVADDVCASAFRSAGQRCSALRLLYLQEEIFDACLATI 830

Query: 866  KGAMDELTLGNPGSVKTDVGPVIDAAAKANLNAHIDHIKQVGRLIHQLSLPEGTENGHFV 925
             GA  EL LG+PG   T +GPVID  AKA L+ ++   +  G +++  + P     G FV
Sbjct: 831  VGAAKELRLGDPGDPATHIGPVIDRGAKAALDDYLARRRAEGSVVYTGAAP---GQGCFV 887

Query: 926  APTAVEIDSIKVLTKENFGPILHVVRYKAAGLQKVIDDINSTGFGLTLGIHSRNEGHALE 985
            AP  V + S + L +E FGP+LHV  ++A     ++ +I +  +GLT+G+HSR E  A  
Sbjct: 888  APHVVRLSSGRELNQEIFGPVLHVAPWRAGDFDSLVAEIMAANYGLTIGLHSRIEARAKR 947

Query: 986  VADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTGPKAGGPHYLTRFVTEKTRTNNITAI 1045
            +A     GN+YINR  IGAVVG QPFGG  LSGTGPKAGG  YL RFV E T T N  A+
Sbjct: 948  LAALAPAGNIYINRTMIGAVVGSQPFGGFNLSGTGPKAGGADYLRRFVREITVTTNTAAL 1007

Query: 1046 GGNATL 1051
            GG+  L
Sbjct: 1008 GGDLRL 1013


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: 2313
Number of extensions: 92
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: 1058
Length of database: 1018
Length adjustment: 45
Effective length of query: 1013
Effective length of database: 973
Effective search space:   985649
Effective search space used:   985649
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: 57 (26.6 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