GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpE in Synechococcus elongatus PCC 7942

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate Synpcc7942_1334 Synpcc7942_1334 aminodeoxychorismate synthase, subunit I

Query= curated2:Q9Z4W7
         (511 letters)



>FitnessBrowser__SynE:Synpcc7942_1334
          Length = 465

 Score =  259 bits (661), Expect = 2e-73
 Identities = 173/452 (38%), Positives = 239/452 (52%), Gaps = 20/452 (4%)

Query: 65  PVTAFAQLCGPDEAGFLLESVPVSGGVARYSYVGHRPVPLEP-----TGGDPLTALRSHL 119
           P  AFA     D    LL+    +   +RY+Y+   P   +      T  DP  AL + L
Sbjct: 21  PQQAFAPFA-QDPHAVLLDLGEPATPESRYAYLCLSPYATQRGDRLVTEADPFQALATSL 79

Query: 120 AR---SVAPVPGLPPFHGGVVGYLGYEAARHFEDLPLAAGPPPGLPESAFLAADDLVVFD 176
           A           LPPF GG+ G+L YE     E LP      P LP  +    D +V  D
Sbjct: 80  ATVDWQTNSDSDLPPFQGGICGFLSYECGAWLERLPTPKPVEPRLPLWSLSLYDLVVACD 139

Query: 177 HATRRVLLMTLYRPARESYDDAVARIVRLNRALRRAPAPAAFSGRPLAAATPADHGTQGW 236
              RR  + +   P ++  D       R  RA +R           L + +P       W
Sbjct: 140 RQQRRTWIFSSGLPLQDPRD-------RQQRAEQRLQWVCDRLQSALPSQSPDWQPQADW 192

Query: 237 TANLTEAQFTERVARAREHIAAGDAFQIVLSR--RLSRPLRARPTDLYRHLRATNPSPYM 294
            A  TEA F + V + + HI AGD FQ  L+   R S+P    P  LYR L   +P P+ 
Sbjct: 193 QALQTEADFCQAVDQVKCHIRAGDIFQANLTTAFRASQPKDLSPWQLYRRLYQLSPEPFS 252

Query: 295 YHLSLGGGRHVIGASPELLVKAE-GRTVRTRPLAGTRPRHPDPAEDLRLERELRADEKER 353
            + + GG   ++  SPE  ++ +    V TRP+ GTRPR  DPA D +L  EL+A EK+R
Sbjct: 253 AYFA-GGDFQLLSVSPERFLRLDRDGWVETRPIKGTRPRSADPAHDRQLATELQASEKDR 311

Query: 354 AEHVMLVDLGRNDLGRVTEPGTVRVERLMRVERFSHVMHLSSTVRGRLAEGRDALDALRS 413
           AE+VM+VDL RNDLGRV  P +++V +L ++E + HV HL+S V G+L  G  A+D LR+
Sbjct: 312 AENVMIVDLLRNDLGRVCRPRSIQVPQLCQLESYEHVHHLTSQVIGQLRSGLTAVDLLRA 371

Query: 414 AFPAGTLSGAPKIRAMEIIAELEPEQRGVYGGALGFVGADGLTDFAIALRTMVVADGHVH 473
            FP G+++GAPKIR+MEII ELEP  R  Y G+L ++G DG  D +I +RT+ ++ G V 
Sbjct: 372 TFPGGSITGAPKIRSMEIIHELEPIPRQAYCGSLFWLGFDGSLDASILIRTLQISQGQVL 431

Query: 474 VQAGAGIVADSDPAAEFRETLHKSRAMLTAVR 505
            QAG GIVADSDP  E  E   K + +L +++
Sbjct: 432 AQAGCGIVADSDPLDECAEMQVKVQPLLRSLQ 463


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: 558
Number of extensions: 26
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: 465
Length adjustment: 34
Effective length of query: 477
Effective length of database: 431
Effective search space:   205587
Effective search space used:   205587
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