GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroG in Shewanella sp. ANA-3

Align 3-deoxy-7-phosphoheptulonate synthase, Trp-sensitive (EC 2.5.1.54) (characterized)
to candidate 7024556 Shewana3_1734 phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq)

Query= ecocyc::AROH-MONOMER
         (348 letters)



>FitnessBrowser__ANA3:7024556
          Length = 354

 Score =  450 bits (1157), Expect = e-131
 Identities = 217/341 (63%), Positives = 267/341 (78%)

Query: 3   RTDELRTARIESLVTPAELALRYPVTPGVATHVTDSRRRIEKILNGEDKRLLVIIGPCSI 62
           +TDELRT+ +  +++PA+LA  YP+T   A ++   RR +E I+ GED+RLLVIIGPCSI
Sbjct: 4   KTDELRTSLLAKVISPAQLASEYPLTQDAADYLVQQRREVEAIIMGEDQRLLVIIGPCSI 63

Query: 63  HDLTAAMEYATRLQSLRNQYQSRLEIVMRTYFEKPRTVVGWKGLISDPDLNGSYRVNHGL 122
           HD  AA++YA RL  L  + +  L I+MR YFEKPRT+VGWKGLISDPDL+GS+  N GL
Sbjct: 64  HDTQAALDYARRLAVLHQELKDDLCILMRVYFEKPRTIVGWKGLISDPDLDGSFEPNKGL 123

Query: 123 ELARKLLLQVNELGVPTATEFLDMVTGQFIADLISWGAIGARTTESQIHREMASALSCPV 182
            +AR+LL Q+ EL +P ATEFLDMV GQ+IADLI+WGAIGARTTESQ+HREMASALSCPV
Sbjct: 124 RIARELLQQITELKLPIATEFLDMVNGQYIADLITWGAIGARTTESQVHREMASALSCPV 183

Query: 183 GFKNGTDGNTRIAVDAIRAARASHMFLSPDKNGQMTIYQTSGNPYGHIIMRGGKKPNYHA 242
           GFKNGTDGN  IAVDA+RAA+  H+F SPDK+G M++Y+T GNPYGHII+RGGKKPNY  
Sbjct: 184 GFKNGTDGNINIAVDAVRAAKVPHIFYSPDKDGAMSVYRTHGNPYGHIILRGGKKPNYFE 243

Query: 243 DDIAAACDTLHEFDLPEHLVVDFSHGNCQKQHRRQLEVCEDICQQIRNGSTAIAGIMAES 302
            DI  A   L   D+   +VVDFSHGN +K H +QL V ++I  Q+R GSTAIAG+MAES
Sbjct: 244 QDIEEARLKLESVDVTPRMVVDFSHGNSEKNHLKQLVVADNIMAQMRAGSTAIAGVMAES 303

Query: 303 FLREGTQKIVGSQPLTYGQSITDPCLGWEDTERLVEKLASA 343
           FL+EG QK+V  QPL YGQSITD CL W+D+E+L+  LA A
Sbjct: 304 FLQEGNQKVVEGQPLCYGQSITDACLHWDDSEKLLRDLAKA 344


Lambda     K      H
   0.320    0.135    0.399 

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: 400
Number of extensions: 7
Number of successful extensions: 1
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: 348
Length of database: 354
Length adjustment: 29
Effective length of query: 319
Effective length of database: 325
Effective search space:   103675
Effective search space used:   103675
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: 49 (23.5 bits)

Align candidate 7024556 Shewana3_1734 (phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq))
to HMM TIGR00034 (3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00034.hmm
# target sequence database:        /tmp/gapView.30938.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00034  [M=342]
Accession:   TIGR00034
Description: aroFGH: 3-deoxy-7-phosphoheptulonate synthase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   6.5e-162  524.0   0.0   7.5e-162  523.8   0.0    1.0  1  lcl|FitnessBrowser__ANA3:7024556  Shewana3_1734 phospho-2-dehydro-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7024556  Shewana3_1734 phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  523.8   0.0  7.5e-162  7.5e-162       1     342 []       6     349 ..       6     349 .. 0.99

  Alignments for each domain:
  == domain 1  score: 523.8 bits;  conditional E-value: 7.5e-162
                         TIGR00034   1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkklaek 77 
                                       d+lr+  + ++++P++l++++plt++aa+ + ++r+e++ i+ G+d+rllv+iGPcsihd +aal+ya+rl+ l ++
  lcl|FitnessBrowser__ANA3:7024556   6 DELRTSLLAKVISPAQLASEYPLTQDAADYLVQQRREVEAIIMGEDQRLLVIIGPCSIHDTQAALDYARRLAVLHQE 82 
                                       68999999********************************************************************* PP

                         TIGR00034  78 lkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldtispqyladllsw 154
                                       lkddl i+mrvyfekPrt+vGWkGli+dPdl++sf+ nkGlriar+ll +++el lp+ate+ld++ +qy+adl++w
  lcl|FitnessBrowser__ANA3:7024556  83 LKDDLCILMRVYFEKPRTIVGWKGLISDPDLDGSFEPNKGLRIARELLQQITELKLPIATEFLDMVNGQYIADLITW 159
                                       ***************************************************************************** PP

                         TIGR00034 155 gaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqvaivetkGnedghiilrGG 231
                                       gaiGarttesqvhre+as+ls+pvgfkngtdG++++a+da+raa+ +h+f s++k+G++++++t+Gn++ghiilrGG
  lcl|FitnessBrowser__ANA3:7024556 160 GAIGARTTESQVHREMASALSCPVGFKNGTDGNINIAVDAVRAAKVPHIFYSPDKDGAMSVYRTHGNPYGHIILRGG 236
                                       ***************************************************************************** PP

                         TIGR00034 232 kkpnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqiaeGekaiiGvmiesnleeGnqsl. 307
                                       kkpny ++d++e++ +le ++ ++++++dfshgns+k++ +ql va+++++q++ G++ai+Gvm es+l+eGnq++ 
  lcl|FitnessBrowser__ANA3:7024556 237 KKPNYFEQDIEEARLKLESVDVTPRMVVDFSHGNSEKNHLKQLVVADNIMAQMRAGSTAIAGVMAESFLQEGNQKVv 313
                                       ***************************************************************************98 PP

                         TIGR00034 308 .keelkyGksvtdacigwedteallrklaeavkerr 342
                                        +++l yG+s+tdac++w+d+e+llr+la+a ++rr
  lcl|FitnessBrowser__ANA3:7024556 314 eGQPLCYGQSITDACLHWDDSEKLLRDLAKASRDRR 349
                                       8899***************************99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (354 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 11.78
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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