GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisI in Desulfovibrio oxyclinae DSM 11498

Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_018123249.1 B149_RS0100770 histidinol dehydrogenase

Query= SwissProt::P00815
         (799 letters)



>NCBI__GCF_000375485.1:WP_018123249.1
          Length = 436

 Score =  236 bits (603), Expect = 1e-66
 Identities = 154/432 (35%), Positives = 243/432 (56%), Gaps = 24/432 (5%)

Query: 370 VQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYF 429
           +Q+ L R     +++  +V  I++ +R +G++AL+EYT KFD  K++   L  P  EE  
Sbjct: 17  IQQWLDRRKDPDTKVDGIVREILDTIRSRGDTALVEYTAKFDCPKITREQLTVP--EEII 74

Query: 430 EGLTE----EMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIP 485
            G  +    E K+ L  +I+NVR FH  Q          + G +  +  RP+++VGLY+P
Sbjct: 75  LGALDSIPAEDKDILAEAIDNVRIFHEKQRENSWWTT-AEDGTILGQMVRPVDRVGLYVP 133

Query: 486 GGTA---ILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLA 542
           GG      L S+ +M  +PAQVA  + I   SPPR+ DG ++P ++  A  +G  +I L+
Sbjct: 134 GGKGGETPLISSLIMNAIPAQVAGVESIAVTSPPRE-DGTLNPYILATAALLGLKEIHLS 192

Query: 543 GGAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIA 602
           G A A+ A+AYGTE+I   D I GPGN FV  AK  +         IDM AGPSE+ ++A
Sbjct: 193 GSAWAIGALAYGTESIAPCDVIAGPGNIFVATAKSQLIGQI----GIDMVAGPSEIAILA 248

Query: 603 DEDADVDFVASDLLSQAEHGIDSQVILV--GVNLSEKKIQEIQDAVHNQALQLPRVDIVR 660
           D+ A+ +++A+D+LSQAEH   +  ILV     L+EK  ++++     Q  +LPR +I  
Sbjct: 249 DDSANPEWLAADMLSQAEHDPLAASILVTDSPELAEKTCEQLK----LQTAELPRGEIAA 304

Query: 661 KCIAH--STIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPES 718
           K +A   +TI++ D    A ++ N+ APEHL L +A+   ++  + +AG++F+G ++PE 
Sbjct: 305 KALADWGATIIVEDLVTGA-DLINRIAPEHLELSLADPWSHLGAIRHAGAIFMGHHSPEP 363

Query: 719 CGDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLD 778
            GDY +G NH LPT    R  S  +   F K  +    +P  +   G  +  +A+ EGL+
Sbjct: 364 VGDYFAGPNHVLPTLRTVRFSSALSVQNFCKKSSVIAASPSYVAEHGDKIARLARLEGLE 423

Query: 779 GHRNAVKIRMSK 790
            H  +V+ R  K
Sbjct: 424 AHARSVECRNKK 435


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: 768
Number of extensions: 44
Number of successful extensions: 7
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: 436
Length adjustment: 37
Effective length of query: 762
Effective length of database: 399
Effective search space:   304038
Effective search space used:   304038
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.

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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