Alignments for a candidate for hisI in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisI in Marinobacter adhaerens HP15

Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate GFF2484 HP15_2428 histidinol dehydrogenase

Query= SwissProt::P00815
         (799 letters)



>FitnessBrowser__Marino:GFF2484
          Length = 434

 Score =  252 bits (643), Expect = 3e-71
 Identities = 147/424 (34%), Positives = 239/424 (56%), Gaps = 17/424 (4%)

Query: 373 ALSRPIQKTSEIMHLVNP----IIENVRDKGNSALLEYTEKFDGVKLSNPV---LNAPFP 425
           AL++ +     + H VN     I+  V+ +G+ A+LE+TEKFD +K+ +     ++    
Sbjct: 18  ALAKLLAWDDSVDHQVNESVRHILHEVKTRGDQAVLEFTEKFDRLKVGSVAELEMDQSRL 77

Query: 426 EEYFEGLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIP 485
           ++  + + ++ + AL+ + E +R +H  Q   ++ + E + G +  +   P+++ GLY+P
Sbjct: 78  QQALDAIPQDQRVALEKAAERIRDYHERQ-NQKSWQYEDEDGTVLGQKVTPLDRAGLYVP 136

Query: 486 GGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGA 545
           GG A  PS+ LM  +PA+VA   E+V   P    DG V+  V+  A   G  ++   GGA
Sbjct: 137 GGKAAYPSSVLMNAIPAKVAGVSEVVMVVPT--PDGVVNDMVLASAAIAGVDRVFTVGGA 194

Query: 546 QAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADED 605
           QAV A+A+GTETIP VDKI+GPGN FV  AK     +   +  IDM AGPSE+LVI+D  
Sbjct: 195 QAVGALAFGTETIPAVDKIVGPGNIFVATAK----REVFGVVGIDMIAGPSEILVISDGK 250

Query: 606 ADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIA- 664
            D D++A DL SQAEH   +Q IL+  +   + +  ++ +++     + R DI+R  +  
Sbjct: 251 TDPDWIAMDLFSQAEHDEQAQSILISPDA--EFLDAVEASINKLLPTMERADIIRTSMTD 308

Query: 665 HSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSS 724
            + ++     ++A E+SN+ APEHL L + +    +  + +AG++F+G YT E+ GDY +
Sbjct: 309 RAALIHVTDLKQAAEVSNRIAPEHLELSVEDPEAMLDDIRHAGAIFMGRYTAEALGDYCA 368

Query: 725 GTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAV 784
           G NH LPT G AR  S      FQK  +    +  G + +GR    +A+ EGL  H  + 
Sbjct: 369 GPNHVLPTSGTARFSSPLGVYDFQKRSSIIGFSAAGADRMGRVASVLARGEGLTAHARSA 428

Query: 785 KIRM 788
           + R+
Sbjct: 429 EYRI 432


Lambda     K      H
   0.315    0.133    0.371 

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: 669
Number of extensions: 31
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: 799
Length of database: 434
Length adjustment: 37
Effective length of query: 762
Effective length of database: 397
Effective search space:   302514
Effective search space used:   302514
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: 42 (22.0 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis