GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisH in Thermophagus xiamenensis HS1

Align imidazole glycerol-phosphate synthase (EC 4.3.2.10) (characterized)
to candidate WP_010527312.1 GQW_RS0107125 imidazole glycerol phosphate synthase subunit HisF

Query= BRENDA::Q9SZ30
         (592 letters)



>NCBI__GCF_000220155.1:WP_010527312.1
          Length = 251

 Score =  144 bits (364), Expect = 3e-39
 Identities = 106/314 (33%), Positives = 155/314 (49%), Gaps = 66/314 (21%)

Query: 280 LAKRVIACLDVRTNDKGDLVVTKGDQYDVREQSNENEVRNLGKPVDLAGQYYKDGADEIS 339
           L+KR+I CLD+R          KG ++         +++ +G PV+L   Y + GADE+ 
Sbjct: 2   LSKRIIPCLDIRNGK-----TVKGVKF--------LDIKEVGDPVELGALYARQGADELV 48

Query: 340 FLNITGFRDF--PLGDLPMIQVLRQTSKNVFVPLTVGGGIRDFTDASGRYYSSLEVAAEY 397
           FL+IT   +      DL    VLR  ++++ +P TVGGGI +  DA              
Sbjct: 49  FLDITASHEKRKTFADL----VLR-IAQHINIPFTVGGGISELKDAE-----------IL 92

Query: 398 FRSGADKISIGSDAVSAAEEFIKSGVKTGKSSLEQISRVYGNQAVVVSIDPRRVYVNHPD 457
             +GADKISI S AV   +             +  +++ +G+Q VVV+ID ++V      
Sbjct: 93  LNAGADKISINSSAVRNPQ------------LISDMAKHFGSQFVVVAIDAKQV------ 134

Query: 458 DVPYKVIRVTNPGPNGEEYAWYQCTVSGGREGRPIGAFELAKAVEELGAGEILLNCIDCD 517
                           E+  W   TV+GGR       F  A+  E+ GAGEIL   +D D
Sbjct: 135 ----------------EDDDWV-VTVNGGRIPTEKRLFSWAREAEDRGAGEILFTSMDHD 177

Query: 518 GQGKGFDIDLVKLISDSVGIPVIASSGAGTPDHFSEVFEKTNASAALAAGIFHRKEVPIQ 577
           G  KGF  + +  +S+ + IP+IAS GAG  +HF +VF    A A LAA IFH  E+PI 
Sbjct: 178 GVKKGFANEALARLSEELSIPIIASGGAGAKEHFKDVFTIGKADAGLAASIFHFNEIPIP 237

Query: 578 SVKEHLQEERIEVR 591
            +K++L+   I VR
Sbjct: 238 ELKDYLRSHNIPVR 251


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: 348
Number of extensions: 28
Number of successful extensions: 7
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: 251
Length adjustment: 30
Effective length of query: 562
Effective length of database: 221
Effective search space:   124202
Effective search space used:   124202
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