GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutH in Mesorhizobium ciceri WSM1271

Align Histidine ammonia-lyase; Histidase; EC 4.3.1.3 (uncharacterized)
to candidate YP_004142202.1 Mesci_3024 phenylalanine/histidine ammonia-lyase

Query= curated2:Q73Q56
         (507 letters)



>NCBI__GCF_000185905.1:YP_004142202.1
          Length = 493

 Score =  286 bits (732), Expect = 1e-81
 Identities = 174/477 (36%), Positives = 260/477 (54%), Gaps = 5/477 (1%)

Query: 6   VTVTGSSLTIEDVVAVARHGAEVKLSADAKKRIKDSKKIVDDIVKSGKPTYGISTGFGEL 65
           + +TG+ + + DV AVAR G +V++  D   R++ +++++D    SG+  YG++TG G  
Sbjct: 4   LVLTGTGVGVGDVAAVARDGRKVEIGPDVIGRLEKARRVLDQAAASGQQIYGLNTGLGA- 62

Query: 66  STVTITKDQNGALQRNLILSHACGVGNPFPEDIVRAIMLLRLNTHASGFSGVTPSVPDIL 125
           +  T  +   GA QR L+   +  VG   P D VRA M  R    + G SG++PSV   L
Sbjct: 63  NLGTAVEGDAGAFQRQLLEGRSGAVGEGLPVDAVRASMAARAAMLSVGGSGLSPSVFVAL 122

Query: 126 VDMLNKGVIPYVPEKGSLGASGDLANLAHIALVMIGEGKAYYEGKLMEGKAALAKAGLKP 185
           VD LN GV P +P  GS+GA GDL  +  +A ++ GEG+A Y+G+ +    AL  A L P
Sbjct: 123 VDALNAGVHPVMPSLGSIGA-GDLVLMTALARMLTGEGEADYQGRRIPAAKALMMARLAP 181

Query: 186 VVLSGKDGLGIINGTPVMSGIGALALHDAEQLLKAANMGASLVFEAFRGITAALDPRIHK 245
           + L+ KDGL +IN + V +G GALA+ DA   L       +L  E F      LDPR+H 
Sbjct: 182 ISLAPKDGLSLINASAVSAGSGALAVTDALTALAQQQHAGALTIEGFGANRTILDPRLHM 241

Query: 246 SRPHKGQIDTAAFILKMLKGSSSINTRENDVQDPYTLRCVPQVHGASADAIAYVRKVLEI 305
           +RP  GQ + A  +  +L    +       +QDP ++RC+  VHGA  +AI   R+ +EI
Sbjct: 242 ARPAAGQQEAAKVLHNLLVRDDA--PAPTTLQDPLSIRCMSSVHGALIEAIGQARQAVEI 299

Query: 306 EINAVTDNPLVFPDNHDVISGGNFHGQPIAITMDFLGIAVSELANISERRIERLVNPQLN 365
           E+NA  DNPLV  D+  V+S GNFH   +A+  + LG+A+++ A     R  +L     N
Sbjct: 300 ELNAAADNPLVLGDDELVLSTGNFHTAALALAFETLGLAIAQCAAAGAARFIQLTGSGRN 359

Query: 366 GGLPAFLIENGGVNSGFMIPQYTAASLVSENKVLAHPASVDSITSSGNKEDHVSMGTTAA 425
            GLP +L   GG ++GF+  Q T  S+++  +  A+P  +D +  S   EDH +    A 
Sbjct: 360 -GLPKYLSPVGGASAGFVPLQKTVTSILAAIRHKANPVMLDFLAVSEGVEDHATQTPLAV 418

Query: 426 RKITEIVKNVRHVLAIEWLTAAQACDLRGVKKYGKGTGEMMKLIRKHISKVTEDRIL 482
            K T ++   R ++A E + AAQA DLR        T  +   IR  +  + EDR L
Sbjct: 419 AKCTGMIALWRRLIAFELMAAAQAIDLRDGFTLAPRTAALHAAIRSLVPMLKEDRPL 475


Lambda     K      H
   0.316    0.134    0.375 

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: 543
Number of extensions: 27
Number of successful extensions: 5
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: 507
Length of database: 493
Length adjustment: 34
Effective length of query: 473
Effective length of database: 459
Effective search space:   217107
Effective search space used:   217107
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 (21.6 bits)
S2: 52 (24.6 bits)

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

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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:

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:

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:

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:

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