GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpE in Desulfovibrio vulgaris Miyazaki F

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate 8501596 DvMF_2315 Chorismate binding-like protein (RefSeq)

Query= curated2:Q9Z4W7
         (511 letters)



>FitnessBrowser__Miya:8501596
          Length = 547

 Score =  146 bits (369), Expect = 2e-39
 Identities = 141/411 (34%), Positives = 186/411 (45%), Gaps = 36/411 (8%)

Query: 118 HLARSVAPVPGLPPFHGGVV-------GYLGYEAARHFEDLPLA-AGPPPGLPESAFLAA 169
           H   ++A   GLPP  G            L ++ AR   D+ L       GLP     +A
Sbjct: 132 HTDAALAAFLGLPPPFGAHSTTPPRDGAPLPWQPARADHDIALGFLAYTYGLPRFGIRSA 191

Query: 170 DDLVVFDHATRRVLLMTLYRPARES-----YDDAVARIV-RLNRALRRAPAPAAFSGRPL 223
              V+     RR   +  + PA  +     + DA   +  R +R L  AP PAAF+    
Sbjct: 192 KPRVLPHALLRRYHAVARWNPATGALTLSVHPDAPPDLTARCSRLLADAPPPAAFTAPNG 251

Query: 224 AAATPADHGTQGWTANLTEAQFTERVARAREHIAAGDAFQIVLSRRLSRPLRARPTD--- 280
            A      G     ++L  A +T  V      I AGD +Q  LS R    L A   D   
Sbjct: 252 CAVFTPSGGCTALPSSLDRAGYTAGVREVLRRIHAGDTYQCNLSTRFG--LHAPGLDSAA 309

Query: 281 LYRHLRATNPSPYMYHLSLGGGRHVIGASPELLVKAE------GRTVRTRPLAGTR---P 331
           L  HL  T P+P+ + L   GGRHV+ ASPE  ++ +      GR V ++P+ GT    P
Sbjct: 310 LSLHLWRTRPAPF-HGLFRIGGRHVVSASPERFLRVDAPGGGPGR-VLSQPIKGTLAFGP 367

Query: 332 RHPDPAEDLRLERELRADEKERAEHVMLVDLGRNDLGRVTEPGTVRVERLMRVERF---- 387
             P P     L   L A  KERAE  M+VDL RND+      G+V V R     R     
Sbjct: 368 GTPHPVWHPGLPGLLAATPKERAELSMIVDLVRNDISADCAHGSVAVARHCATFRVGGAA 427

Query: 388 SHVMHLSSTVRGRLAEGRDALDALRSAFPAGTLSGAPKIRAMEIIAELEPEQRGVYGGAL 447
           S ++ + S V G L   R  LD L SAFP G+++G PK R + II   EP  R VY G+L
Sbjct: 428 SGLVQMYSDVTGTLRPERTCLDLLLSAFPGGSVTGCPKRRTLAIIEAGEPHSREVYCGSL 487

Query: 448 GFVGADGLTDFAIALRT--MVVADGHVHVQAGAGIVADSDPAAEFRETLHK 496
             +      D +IA+RT     A G     AG+GIV DSDP +E+ ET  K
Sbjct: 488 LAIADARTMDASIAIRTGWHDAATGRFEHCAGSGIVVDSDPESEYEETWAK 538


Lambda     K      H
   0.319    0.134    0.394 

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: 784
Number of extensions: 45
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: 511
Length of database: 547
Length adjustment: 35
Effective length of query: 476
Effective length of database: 512
Effective search space:   243712
Effective search space used:   243712
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: 52 (24.6 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