GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Pseudomonas fluorescens FW300-N2E2

Align Salicylate synthase; Chorismate mutase; CM; EC 5.4.99.5; Isochorismate synthase/isochorismate lyase; EC 4.2.99.21; EC 5.4.4.2; Mycobactin synthase protein (uncharacterized)
to candidate Pf6N2E2_4822 Anthranilate synthase, aminase component (EC 4.1.3.27)

Query= curated2:Q73XV3
         (450 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4822
          Length = 493

 Score =  140 bits (353), Expect = 9e-38
 Identities = 93/275 (33%), Positives = 137/275 (49%), Gaps = 7/275 (2%)

Query: 170 PGL--RDASAVDVVTDPSNYRD---RVASAVAE-IAAGRYHKVILSRCLQVPFAVDFPST 223
           PGL     SA D V   S  +D   R    + E I AG   +V+ S+ + + F       
Sbjct: 203 PGLDFSKQSATDPVFRSSFTQDDYERAVDTIKEYILAGDCMQVVPSQRMSIDFKAAPIDL 262

Query: 224 YRLARRHNTPVRSFLLRLGGIRAVGYSPELVAAVRHDGVVVTEPLAGTRAFGRGALHDRQ 283
           YR  R  N     +    G    VG SPE++  V  D ++   P+AGTR  G     DR 
Sbjct: 263 YRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVE-DNLITVRPIAGTRPRGATEEADRA 321

Query: 284 ARDDLESNSKEIVEHAISVRSSLQEMAEIAEPGTAVVTDFMTVRERGSVQHLGSTVSGRL 343
             +DL S+ KEI EH + +     +   ++E G+  +T+ M +    +V H+ S V+G+L
Sbjct: 322 LEEDLLSDDKEIAEHLMLIDLGRNDTGRVSEIGSVKLTEKMVIERYSNVMHIVSNVTGQL 381

Query: 344 GTSNDRMDALEALFPAVTASGIPKAGGVEAILRLDEGPRGLYSGAVVMVSADGALDAALT 403
                 MDAL A+ PA T SG PK   +E I  L+   RG+Y GAV   + +G +D A+ 
Sbjct: 382 KAGLTAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKRGVYGGAVGYFAWNGNMDTAIA 441

Query: 404 LRAAYEHDGKTWLRAGAGIIEESTPEREFEETCEK 438
           +R A   +G+  ++AG GI+ +S P  E+EET  K
Sbjct: 442 IRTAVIKNGELHVQAGGGIVADSVPALEWEETLNK 476


Lambda     K      H
   0.318    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: 429
Number of extensions: 23
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: 450
Length of database: 493
Length adjustment: 33
Effective length of query: 417
Effective length of database: 460
Effective search space:   191820
Effective search space used:   191820
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: 51 (24.3 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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