GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisC in Alkalihalobacterium alkalinitrilicum DSM 22532

Align histidine transaminase (EC 2.6.1.38) (characterized)
to candidate WP_078428542.1 BK574_RS10305 threonine-phosphate decarboxylase CobD

Query= BRENDA::Q8R5Q4
         (351 letters)



>NCBI__GCF_002019605.1:WP_078428542.1
          Length = 360

 Score =  159 bits (402), Expect = 1e-43
 Identities = 107/330 (32%), Positives = 181/330 (54%), Gaps = 20/330 (6%)

Query: 30  NETPFELPEEVMKNIGDIVKSIHVNIYPDPTAEKLREELARYCSVTPKNIFVGNGSDEII 89
           N  P  +P  V       +++I    YPDP A +LRE+LA   +V+   + VGNG+ E+I
Sbjct: 31  NVNPLGVPRVVRDRWNQYIEAI--TTYPDPHASQLREKLANDLNVSIDQLIVGNGAAELI 88

Query: 90  HLIMLAFVDKGDTVLYPHPSFAMYSIYSKIAGANEIAVNLNEDYTYN--VERFAEAVERY 147
            LI   F  K   VL   P+F+ Y           I   L ++ +++  VE   EA+   
Sbjct: 89  LLIANYFRKK--RVLIVEPTFSEYRDACLTYDCEIIRYQLLQESSWDIQVESLLEAINGV 146

Query: 148 KPKLVFLCNPNNPTGSVIDEEDIIRIIEKARG---IVIVDEAYFEFYGK--TLVPYIDRF 202
              ++FLC+PNNPTG+ I+   +I++  +AR     VI+DEA+++F  +  +++PYI+ F
Sbjct: 147 D--ILFLCHPNNPTGTTIERSTLIQVFSRAREKNVTVIIDEAFYDFCTENVSVIPYIEEF 204

Query: 203 ENLIVLRTLSKAFGIAGLRVGYALSNGEIVKYLNLVKSPYNLNSLSQRIALEVLKSGV-L 261
            NL+VLR+L+K + I  LR+GY ++  E V  L   + P+++N ++Q++ L+ +      
Sbjct: 205 HNLVVLRSLTKMYAIPSLRLGYVVARKEFVSELKKFQQPWSVNGMAQQVGLDCISDEEHA 264

Query: 262 KERVNYIINEREKLVKELNKINGIKVYPSHANFVLCKFENAND----VHKRLVERGILVR 317
            +   +I  ER+++ K L+ I G +V PS  NF L K +  N+    +   L+  G++ R
Sbjct: 265 IDTKTFIREERKRMFKLLSDI-GYEVSPSVVNFYLLKPKGTNEDLTPLITFLIRNGVIPR 323

Query: 318 NFSNVKGLEGT-LRITVSSSDANDYLINAL 346
           +  N  GLEG  +R+ + +   ND L++ L
Sbjct: 324 HTYNFLGLEGKYIRLAIKTRQDNDLLLSVL 353


Lambda     K      H
   0.319    0.138    0.389 

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: 301
Number of extensions: 17
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: 351
Length of database: 360
Length adjustment: 29
Effective length of query: 322
Effective length of database: 331
Effective search space:   106582
Effective search space used:   106582
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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.

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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