GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisI in Methylosarcina fibrata AML-C10

Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_020564986.1 A3OW_RS0118680 histidinol dehydrogenase

Query= SwissProt::P00815
         (799 letters)



>NCBI__GCF_000372865.1:WP_020564986.1
          Length = 434

 Score =  235 bits (600), Expect = 3e-66
 Identities = 142/409 (34%), Positives = 222/409 (54%), Gaps = 13/409 (3%)

Query: 383 EIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNP-VLNAPFP--EEYFEGLTEEMKEA 439
           ++   V  I+ ++R +G+ AL+EYT +FD  +++    L  P    ++ ++GL ++  +A
Sbjct: 33  DVHRRVIDILADIRSRGDQALVEYTNRFDRRQITQAGELEMPKAVLKQAWDGLPQDQAKA 92

Query: 440 LDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALMLG 499
           L  + + +R + A      + E     G +  +   P+++VGLY+PGG A  PS+ LM  
Sbjct: 93  LQTAADRIRAY-AEHQKMASWEFTEADGTVLGQKITPLDRVGLYVPGGKAAYPSSVLMNA 151

Query: 500 VPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIP 559
           +PA+VA   E++   P     G+ +  V+  A   G  ++   GGAQAVAA+AYGT TIP
Sbjct: 152 IPAKVAGVAELIMVVPT--PGGEANSMVLAAAWLAGVDRVFTVGGAQAVAALAYGTGTIP 209

Query: 560 KVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQA 619
            V KI+GPGN +V  AK  V         IDM AGPSE+L+I D   D D++A DL SQA
Sbjct: 210 PVAKIVGPGNIYVATAKKLVFGQV----GIDMIAGPSEILIICDGKTDPDWIAMDLFSQA 265

Query: 620 EHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAH-STIVLCDGYEEAL 678
           EH  ++Q IL+  +     +  ++ ++      + R DI+R  +     ++  D    A 
Sbjct: 266 EHDENAQAILISDDPGF--LDAVEASIRRLLPTMERADIIRASLTERGALIRVDHLLVAA 323

Query: 679 EMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQ 738
            ++N+ APEHL L +A      + + +AG++F+G YT E+ GDY +G NH LPT G AR 
Sbjct: 324 SVANRIAPEHLELSVAEPEALSRHIRHAGAIFMGRYTAEALGDYCAGPNHVLPTSGTARF 383

Query: 739 YSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIR 787
            S      FQK  +  N +P G   +GRA   +A+ E L  H  + + R
Sbjct: 384 SSPLGVYDFQKRTSLINCSPAGARTLGRAASILARGEQLTAHARSAEYR 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: 702
Number of extensions: 35
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 Apr 10 2024. The underlying query database was built on Apr 09 2024.

Links

Downloads

Related tools

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