GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisH in Phyllobacterium brassicacearum STM 196

Align imidazole glycerol-phosphate synthase (EC 4.3.2.10) (characterized)
to candidate WP_106713387.1 CU102_RS22810 imidazole glycerol phosphate synthase subunit HisF

Query= BRENDA::Q9SZ30
         (592 letters)



>NCBI__GCF_003010955.1:WP_106713387.1
          Length = 261

 Score =  144 bits (364), Expect = 3e-39
 Identities = 109/313 (34%), Positives = 150/313 (47%), Gaps = 58/313 (18%)

Query: 280 LAKRVIACLDVRTNDKGDLVVTKGDQYDVREQSNENEVRNLGKPVDLAGQYYKDGADEIS 339
           L  RVI CLDV+     D  V KG         N  ++ + G PV+ A  Y   GADE+ 
Sbjct: 3   LKARVIPCLDVK-----DGRVVKG--------VNFVDLIDAGDPVEAAKAYDAAGADELC 49

Query: 340 FLNITGFRDFPLGDLPMIQVLRQTSKNVFVPLTVGGGIRDFTDASGRYYSSLEVAAEYFR 399
           FL+IT   D       +  V+ +T++  F+PLTVGGG+R   D             +   
Sbjct: 50  FLDITASSD---NRETIFDVVARTAEQCFMPLTVGGGVRTVADIR-----------KLLL 95

Query: 400 SGADKISIGSDAVSAAEEFIKSGVKTGKSSLEQISRVYGNQAVVVSIDPRRVYVNHPDDV 459
           +GADK+SI + AV+  E   ++  K            +GNQ +VV+ID ++V        
Sbjct: 96  AGADKVSINTAAVNNPEFIAEAADK------------FGNQCIVVAIDAKKV-------- 135

Query: 460 PYKVIRVTNPGPNGEEYAWYQCTVSGGREGRPIGAFELAKAVEELGAGEILLNCIDCDGQ 519
                        GE   W +    GGR    I A E A+ V +LGAGEILL  +D DG 
Sbjct: 136 ----------SATGETDRW-EIFTHGGRHATGIDAIEFARRVVDLGAGEILLTSMDRDGS 184

Query: 520 GKGFDIDLVKLISDSVGIPVIASSGAGTPDHFSEVFEKTNASAALAAGIFHRKEVPIQSV 579
             G+DI + + I+D+V +PVIAS G G  DH  E   + +ASA LAA IFH     I   
Sbjct: 185 KIGYDIPVTRAIADAVRVPVIASGGVGNLDHMVEGIIEGHASAVLAASIFHFGTYTIAQA 244

Query: 580 KEHLQEERIEVRI 592
           K H+    I +R+
Sbjct: 245 KAHMAAAGIPMRL 257


Lambda     K      H
   0.317    0.135    0.391 

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: 346
Number of extensions: 20
Number of successful extensions: 6
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: 592
Length of database: 261
Length adjustment: 31
Effective length of query: 561
Effective length of database: 230
Effective search space:   129030
Effective search space used:   129030
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 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Jul 26 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