Alignments for a candidate for aroA in Chlorobium phaeobacteroides BS1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Chlorobium phaeobacteroides BS1

Align 5-enolpyruvoylshikimate-3-phosphate synthase (EC 2.5.1.19) (characterized)
to candidate 642684662 Cphamn1_2175 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19)

Query= metacyc::AROEBACSU-MONOMER
         (428 letters)



>IMG__ChlphaBS1_FD:642684662
          Length = 435

 Score =  286 bits (733), Expect = 7e-82
 Identities = 172/430 (40%), Positives = 253/430 (58%), Gaps = 16/430 (3%)

Query: 11  GEIH-IPGDKSISHRSVMFGALAAGTTTVKNFLPGADCLSTIDCFRKMGVHIEQS----- 64
           GE++ +P DKSI+HR+ + GA+A GTT + NF  G D  ST+   +  G+ + Q      
Sbjct: 6   GEVNALPPDKSIAHRAALIGAVADGTTEISNFSGGFDNQSTLGVLQACGIAVHQEKLKGP 65

Query: 65  ----SSDVVIHGKGIDALKEPESLLDVGNSGTTIRLMLGILAGRPFYSAVAGDESIAKRP 120
               S +VVIH +G  +L  PE  L   NSG+T+R+  GILA +PF S +AGD S+ KRP
Sbjct: 66  NGLISRNVVIHAQGFWSLSRPEKDLMCNNSGSTMRMFAGILAAQPFESRLAGDSSLMKRP 125

Query: 121 MKRVTEPLKKMGAKIDGRAGGEFTPLSVSGAS-LKGIDYVSPVASAQIKSAVLLAGLQAE 179
           M+RV  PL+ MGA +   +     P+++ G + L+ IDY  PV SAQ+KS V LA L AE
Sbjct: 126 MQRVAHPLRLMGADV-ALSSDNTAPVAIRGTTHLRPIDYELPVPSAQVKSLVALAALHAE 184

Query: 180 GTTTVTEPHKSRDHTERMLSAFGVKLSEDQTSVSIAGGQKLTAADIFVPGDISSAAFFLA 239
           G + V E   SR+HTE ML      LS+ +++V I G + + A    +PGD S+A F +A
Sbjct: 185 GESRVIETLPSRNHTELMLGLKVEALSDGRSAVIIPGRKTVPAKPFHIPGDPSAACFIIA 244

Query: 240 AGAMVPNSRIVLKNVGLNPTRTGIIDVLQNMGAKLEIKPSADSGAEPYGDLIIETS-SLK 298
            G +   S IV+++V LNPTRTG + VL   GA++ ++    +G E  GD+++  S S+K
Sbjct: 245 LGLLSAGSEIVVRDVCLNPTRTGYMGVLLGAGAEISMENIRFAGGEKIGDVLVRHSPSMK 304

Query: 299 AVEIGGD-IIPRLIDEIPIIALLATQAEGTTVIKDAAELKVKETNRIDTVVSELRKLGAE 357
            + I    ++   IDEIP++A+L+  A G   + +AAEL+ KE++RI  VV  L ++G  
Sbjct: 305 PLSISDPAVVANSIDEIPMLAVLSACATGAFELYNAAELRAKESDRISAVVDNLERIGFV 364

Query: 358 IEPTADGMKVYGKQ--TLKGGAAVSSHGDHRIGMMLGIASCITEEPIEIEHTDAIHVSYP 415
            +  ADG  V G++  T  G  A+ S+ DHRI M   IA  +    ++I     I VS+P
Sbjct: 365 CDEYADGFAVTGRKDVTPTGKVAIDSYDDHRIAMSFAIADRVVPMELDISDAKVIGVSFP 424

Query: 416 TFFEHLNKLS 425
            FFE +  L+
Sbjct: 425 DFFEIIESLA 434


Lambda     K      H
   0.315    0.133    0.368 

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: 435
Number of extensions: 23
Number of successful extensions: 6
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: 428
Length of database: 435
Length adjustment: 32
Effective length of query: 396
Effective length of database: 403
Effective search space:   159588
Effective search space used:   159588
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: 42 (22.0 bits)
S2: 51 (24.3 bits)

Align candidate 642684662 Cphamn1_2175 (3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19))
to HMM TIGR01356 (aroA: 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19))

# 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/TIGR01356.hmm
# target sequence database:        /tmp/gapView.56013.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01356  [M=415]
Accession:   TIGR01356
Description: aroA: 3-phosphoshikimate 1-carboxyvinyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                    -----------
   1.8e-105  339.0   0.0   2.1e-105  338.8   0.0    1.0  1  IMG__ChlphaBS1_FD:642684662  


Domain annotation for each sequence (and alignments):
>> IMG__ChlphaBS1_FD:642684662  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  338.8   0.0  2.1e-105  2.1e-105       4     412 ..      10     433 ..       6     435 .] 0.91

  Alignments for each domain:
  == domain 1  score: 338.8 bits;  conditional E-value: 2.1e-105
                    TIGR01356   4 kipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.ee.ke.......elviegvgg..lkepeaeld 74 
                                  ++p++KSi+hRa l++a a+g+t++ n+  + D ++tl +l++ G+ v+ e+ k+       ++vi+ +g   l +pe+ l 
  IMG__ChlphaBS1_FD:642684662  10 ALPPDKSIAHRAALIGAVADGTTEISNFSGGFDNQSTLGVLQACGIAVHqEKlKGpnglisrNVVIHAQGFwsLSRPEKDLM 91 
                                  47**********************************************944343332333334666665557799999**** PP

                    TIGR01356  75 lgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgplkg.givelsgsaSsQy 155
                                  ++nsG t+R+  g+la++++e+ l gd sl kRP++r+ ++Lr +ga++  ++ ++++P+ai+g+ ++ +i +  +  S+Q+
  IMG__ChlphaBS1_FD:642684662  92 CNNSGSTMRMFAGILAAQPFESRLAGDSSLMKRPMQRVAHPLRLMGADVALSS-DNTAPVAIRGTTHLrPIDYELPVPSAQV 172
                                  **************************************************877.68*********8888************* PP

                    TIGR01356 156 ksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeederkivvkggqkykqkevevegDaSsAafflaaaa 237
                                  ks + laa   l+a++++ v+e l sr+++e++L l  ++   ++    + ++++g ++   k ++++gD+S+A+f++a+++
  IMG__ChlphaBS1_FD:642684662 173 KSLVALAA---LHAEGESRVIETLPSRNHTELMLGLKVEA---LSD-GRSAVIIPGRKTVPAKPFHIPGDPSAACFIIALGL 247
                                  ********...8999******************9764444...444.44588999888855556****************** PP

                    TIGR01356 238 itge.evtvenlgenstqgdkaiiivLeemGadveveeqr........dvevegasklkgvkv.d.idvdsliDelptlavl 308
                                  ++ + e++v+++  n+t+++   + vL   Ga++++e+ r        dv v+++ ++k++ + d + v++ iDe+p+lavl
  IMG__ChlphaBS1_FD:642684662 248 LSAGsEIVVRDVCLNPTRTG--YMGVLLGAGAEISMENIRfaggekigDVLVRHSPSMKPLSIsDpAVVANSIDEIPMLAVL 327
                                  **999***************..556**************************************95599************** PP

                    TIGR01356 309 aafAegetriknieelRvkEsdRiaaiaeeLeklGveveeledgllieGkk..kelkgavvdtydDHRiamalavlglaaeg 388
                                  +a+A g  +++n++elR+kEsdRi+a++++Le++G  ++e +dg+ ++G+k  +   +  +d+ydDHRiam++a++  ++  
  IMG__ChlphaBS1_FD:642684662 328 SACATGAFELYNAAELRAKESDRISAVVDNLERIGFVCDEYADGFAVTGRKdvTPTGKVAIDSYDDHRIAMSFAIADRVVPM 409
                                  **************************************************8755555689********************** PP

                    TIGR01356 389 eveiedaecvaksfPeFfevleql 412
                                  e+ i da+++ +sfP+Ffe +e+l
  IMG__ChlphaBS1_FD:642684662 410 ELDISDAKVIGVSFPDFFEIIESL 433
                                  *********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (435 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 26.70
//
[ok]

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis