GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisH in Sulfurihydrogenibium subterraneum DSM 15120

Align imidazole glycerol-phosphate synthase (EC 4.3.2.10) (characterized)
to candidate WP_028950472.1 Q385_RS0104230 imidazole glycerol phosphate synthase subunit HisF

Query= BRENDA::Q9SZ30
         (592 letters)



>NCBI__GCF_000619805.1:WP_028950472.1
          Length = 252

 Score =  181 bits (460), Expect = 2e-50
 Identities = 124/316 (39%), Positives = 177/316 (56%), Gaps = 68/316 (21%)

Query: 280 LAKRVIACLDVRTNDKGDLVVTKGDQYDVREQSNENEVRNLGKPVDLAGQYYKDGADEIS 339
           LAKR+I CLDV   +KG +V  KG         N   + + G PV++A  Y K+GADEI 
Sbjct: 2   LAKRIIPCLDV---NKGRVV--KG--------VNFVNLIDAGDPVEIAAAYDKEGADEIV 48

Query: 340 FLNITGF---RDFPLGDLPMIQVLRQTSKNVFVPLTVGGGIRDFTDASGRYYSSLEVAAE 396
           FL+IT     RD       ++ V+++T++ VF+PLTVGGG+R           SLE   +
Sbjct: 49  FLDITASAEDRDI------ILDVVKKTAETVFMPLTVGGGVR-----------SLEDIRK 91

Query: 397 YFRSGADKISIGSDAVSAAEEFIKSGVKTGKSSLEQISRVYGNQAVVVSIDPRRVYVNHP 456
              +GADK+SI + AV               S +E  +  +G+  +VV+ID +++     
Sbjct: 92  LLENGADKVSINTAAVK------------NPSLVESAAVRFGSSTIVVAIDAKKI----- 134

Query: 457 DDVPYKVIRVTNPGPNGEEYAWYQCTVSGGREGRPIGAFELAKAVEELGAGEILLNCIDC 516
                            +E  W +  ++GGR    I A + AKAVE+LGAGEILL  +D 
Sbjct: 135 -----------------DENKW-EVYINGGRTPTGIDAVQWAKAVEDLGAGEILLTSMDK 176

Query: 517 DGQGKGFDIDLVKLISDSVGIPVIASSGAGTPDHFSEVFEKTNASAALAAGIFHRKEVPI 576
           DG   G+D++L K +S++V IPVIAS GAG  +HF EVFE+  A AALAA +FH KEV I
Sbjct: 177 DGTKSGYDVELTKAVSEAVKIPVIASGGAGKKEHFYEVFEEGKADAALAASLFHFKEVGI 236

Query: 577 QSVKEHLQEERIEVRI 592
           + +K+ L+E+ + VRI
Sbjct: 237 KELKQFLKEKNVNVRI 252


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: 362
Number of extensions: 28
Number of successful extensions: 8
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: 252
Length adjustment: 30
Effective length of query: 562
Effective length of database: 222
Effective search space:   124764
Effective search space used:   124764
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 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