GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpE in Trichormus variabilis ATCC 29413

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate WP_041456890.1 AVA_RS17560 aminodeoxychorismate synthase component I

Query= SwissProt::P20579
         (493 letters)



>NCBI__GCF_000204075.1:WP_041456890.1
          Length = 711

 Score =  229 bits (584), Expect = 2e-64
 Identities = 141/377 (37%), Positives = 203/377 (53%), Gaps = 19/377 (5%)

Query: 115 FNGGLVGYFGYDCVRYVEKRLGVSPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVD 174
           FN G VGYFGY+      K    S    P   PD +L++SD ++ FD+     + + L  
Sbjct: 327 FNCGFVGYFGYEL-----KAESGSGLEHPSSCPDAILLLSDRLIAFDHQEQTTYLVYLAP 381

Query: 175 PAE----EQAFEQGQARLQGLLETLRQPITPRRGLDLSGPQAAEPEFRSSYTREDYENAV 230
             E    +  FE  + RL+ L      P+ P      S P      FR S + + Y++ +
Sbjct: 382 VGETAPAKDWFEITEKRLRTL-----PPLPPLVPSTTSHPVT----FRLSRSYQTYKDDI 432

Query: 231 GRIKEYILAGDCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSP 290
            R  + I  G+  QV  + ++  D    P+  YR LR  NP PY  F  FG+  +  SSP
Sbjct: 433 SRCLKEIREGETYQVCLTNQLRTDTTTDPLTFYRRLRQVNPAPYSAFLRFGEMAIACSSP 492

Query: 291 EVLVRVE-DNLVTVRPIAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVGR 349
           E  ++++    V  +PI GT  RG T E D  L + L S +KE AE+LM++DL RND+GR
Sbjct: 493 ERFLQIDRQGWVETKPIKGTVRRGETPEEDFLLRESLRSSEKEQAENLMIVDLLRNDLGR 552

Query: 350 VSSTGSVRLTEKMVIERYSNVMHIVSNVAGQLREGLTAMDALRAILPAGTLSGAPKIRAM 409
           V   GS+ + + M +E Y+ V  +VS + G L   + A D +R   P G+++GAPK+R M
Sbjct: 553 VCQVGSIHVPKLMDVESYATVHQLVSTIRGFLSPDMDATDCIRMAFPGGSMTGAPKLRTM 612

Query: 410 EIIDELEPVKRGVYGGAVGYFAWNGNMDTAIAIRTAVINDGELHVQAGGGIVADSVPALE 469
           EIID+LE   RGVY GA+G+   NG  D  I IRTAV+   +  +  GGGIVA S   +E
Sbjct: 613 EIIDQLEQEARGVYSGAIGFLGVNGAADLNIVIRTAVLTPNQTSIGIGGGIVALSEVEME 672

Query: 470 WEETINKRRAMFRAVAL 486
           ++ETI K  A+ +A+ L
Sbjct: 673 FQETILKADALIQAMLL 689


Lambda     K      H
   0.320    0.138    0.403 

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: 816
Number of extensions: 60
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: 493
Length of database: 711
Length adjustment: 37
Effective length of query: 456
Effective length of database: 674
Effective search space:   307344
Effective search space used:   307344
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 (21.8 bits)
S2: 53 (25.0 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