GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cimA in Azoarcus olearius BH72

Align 2-isopropylmalate synthase / (R)-citramalate synthase; EC 2.3.1.182; EC 2.3.3.13 (characterized, see rationale)
to candidate WP_011767245.1 AZO_RS17695 2-isopropylmalate synthase

Query= uniprot:D4GSQ2
         (512 letters)



>NCBI__GCF_000061505.1:WP_011767245.1
          Length = 572

 Score =  107 bits (268), Expect = 9e-28
 Identities = 100/315 (31%), Positives = 146/315 (46%), Gaps = 29/315 (9%)

Query: 202 STHTHDDLGLAMANVHASLAAGADLVHTTVNGIGERAGNVALEEVAIALDHCYDVESVKL 261
           S H H+D G A+A    ++ AGAD V   + G GER GNV L  +A+ L        +  
Sbjct: 250 SVHPHNDRGTAVAAAELAVMAGADRVEGCLFGNGERTGNVDLVTLALNLYSQGVHPGLDF 309

Query: 262 DELYALAQKVAQATGVSLPPNKAVVGQNAFTHESGIHTDGTLK------DDAMYE----P 311
             +  +A+ V   T + + P    VG   FT  SG H D   K       DA++E    P
Sbjct: 310 SRINEVARTVEHCTQLPIHPRHPYVGDLVFTAFSGSHQDAIKKGFAVQQPDAVWEVPYLP 369

Query: 312 YPPETVGR--ERRLVLGKHAGRAGVKAALD-EHGV---DATDEEVAAVVERVKELGDRGK 365
             P  +GR  E  + +   +G+ G+   L+ E+G+        E +A ++R+ +  +RG 
Sbjct: 370 VDPADLGRSYESIIRVNSQSGKGGIAYLLEAEYGLVMPRRLQVEFSAAIQRITD--ERGT 427

Query: 366 RVTDADL-LAFAEDVQGRERARQVELLDLTAASGGGTPTASVRLRVEGEERVASGTGSGP 424
            ++  D+  AF E+      A     ++   A  GG    S+ +   G  RV  G G+GP
Sbjct: 428 ELSAGDIWRAFEEEYLA--VAAPYAYVEHHLAEHGGQQGISLTVEEAGVRRVLRGVGNGP 485

Query: 425 VDAAVKAVREALGPDADAQLDEYHVDAITGGTD--AVVTVEVTMSLGDRSVSVAASHADI 482
           +DAA+ A+      DA A L  Y   AI  G D  AV  +E+    G  S      HA+I
Sbjct: 486 IDAALHAL------DAGAVLLGYEERAIGQGGDARAVAYIELADGEGGGSTFGVGIHANI 539

Query: 483 TRASVQAMVDALDRL 497
             ASV A+V ALDRL
Sbjct: 540 VTASVLAIVSALDRL 554


Lambda     K      H
   0.312    0.129    0.361 

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: 707
Number of extensions: 43
Number of successful extensions: 4
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: 512
Length of database: 572
Length adjustment: 35
Effective length of query: 477
Effective length of database: 537
Effective search space:   256149
Effective search space used:   256149
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 52 (24.6 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:

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