GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hcs in Thermocrinis albus DSM 14484

Align Homocitrate synthase 1; EC 2.3.3.14 (uncharacterized)
to candidate WP_012991460.1 THAL_RS02075 homocitrate synthase

Query= curated2:Q44290
         (377 letters)



>NCBI__GCF_000025605.1:WP_012991460.1
          Length = 316

 Score =  223 bits (569), Expect = 4e-63
 Identities = 128/317 (40%), Positives = 190/317 (59%), Gaps = 2/317 (0%)

Query: 3   KVLINDTTLRDGEQAAGVVFTLEEKVAIAKFLDTIGVPELEVGIPAMGEEEMRAICAISN 62
           +V I DTTLR+G Q+  +  +LEE+ A+   L ++   E+EVG+PA GEEE   I  ++ 
Sbjct: 2   RVYITDTTLREGIQSPSLELSLEERYALFNHLVSLNFYEIEVGVPAKGEEEREYIRKLTK 61

Query: 63  LGLKANLLAWNRAVISDIKASVACGMERVHIAIPVSGIQIAAKFHGQWRVSLQRLKDCIS 122
                 ++ WNRA I DI+ S++C +++V +A PVS I I  K            K+ + 
Sbjct: 62  GEHADRVIVWNRANIKDIEYSLSCNVKKVEVAFPVSDIMIEKKLRKSREYLKGLAKEIVP 121

Query: 123 FAVDQGLWVAVGGEDSSRADENFLLDVALYAQEWGASRFRFCDTVGVLDPFTTYGKVKLL 182
              ++GL+++VG ED+SRAD NFLL+     +  GA R R  DTVGV++P +    VK L
Sbjct: 122 CCKEKGLYLSVGLEDASRADYNFLLEFVELVKTHGADRVRLSDTVGVMNPLSVAKVVKDL 181

Query: 183 VSALTIPVEVHTHNDFGMATANALAGIKAGASSVNTTVIGLGERAGNAALEEVVMAIKRI 242
            S +T  VEVH HNDFGMATANA+  + +GA  VN++++GLGER G    EEVV+ ++ I
Sbjct: 182 -SNIT-DVEVHFHNDFGMATANAVVAVMSGAKFVNSSLLGLGERCGITPTEEVVIYLEVI 239

Query: 243 YGVDMGIDTPRLLELSQLVAAASGANVPPWKAIVGENTFAHESGIHAHGVLQNPDTYEPF 302
            G++ GID  +L E  +     +G  V   K I+G N F ++S IH  G+ ++ DTY PF
Sbjct: 240 LGINTGIDIRKLYEKIREFVNMTGIKVHDNKPIIGTNAFTNKSRIHIDGLSKSKDTYLPF 299

Query: 303 APEEVGWERRLVVGKHS 319
            P+ +G   ++  G +S
Sbjct: 300 DPQLIGEMSKICKGYYS 316


Lambda     K      H
   0.318    0.133    0.388 

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: 300
Number of extensions: 11
Number of successful extensions: 2
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: 377
Length of database: 316
Length adjustment: 29
Effective length of query: 348
Effective length of database: 287
Effective search space:    99876
Effective search space used:    99876
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 (21.7 bits)
S2: 49 (23.5 bits)

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