Alignments for a candidate for aroA in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Caulobacter crescentus NA1000

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate CCNA_03704 CCNA_03704 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::C3MC80
         (448 letters)



>FitnessBrowser__Caulo:CCNA_03704
          Length = 443

 Score =  441 bits (1135), Expect = e-128
 Identities = 251/448 (56%), Positives = 299/448 (66%), Gaps = 16/448 (3%)

Query: 4   GLSPRPATAKKSADLKGTVRIPGDKSISHRSFMFGGLASGETRITGLLEGEDVINTGKAM 63
           GL   P  A     L+G VR PGDKSISHRS + G LA+G T + GLLEG+DV+ T +AM
Sbjct: 5   GLKSAPGGA-----LRGIVRAPGDKSISHRSMILGALATGTTTVEGLLEGDDVLATARAM 59

Query: 64  QAMGAKIRKEG-DTWIINGVGNGALLAPEAPLDFGNAGTGCRLTMGLVGVYDFDSTFIGD 122
           QA GA+I +EG   W I G   G    P   +D GNAGTG RL MG    +   +TF GD
Sbjct: 60  QAFGARIEREGVGRWRIEG--KGGFEEPVDVIDCGNAGTGVRLIMGAAAGFAMCATFTGD 117

Query: 123 ASLTKRPMGRVLDPLREMGVQVKSAEGDRLPVTLRGPKTPNPITYRVPMASAQVKSAVLL 182
            SL  RPMGRVLDPL  MG      +  RLP+TL+G      + Y +PMASAQVKSAVLL
Sbjct: 118 QSLRGRPMGRVLDPLARMGATWLGRDKGRLPLTLKGGNLRG-LNYTLPMASAQVKSAVLL 176

Query: 183 AGLNTPGITTVIEPVMTRDHTEKMLQGFGANLSVETDTAGVRT---IRLEGRGKLTGQVI 239
           AGL+  G   VIEP  TRDHTE+ML+ FGA + VE   AG +T   +RL    KLTG  +
Sbjct: 177 AGLHAEGGVEVIEPEATRDHTERMLRAFGAEVIVEDRKAGDKTFRHVRLPEGQKLTGTHV 236

Query: 240 DVPGDPSSTAFPLVAALLVPGSDVTILNVLMNPTRTGLILTLQEMGANIEVMNPRLAGGE 299
            VPGDPSS AFPLVAAL+VPGS+VT+  V++N  RTGL  TLQEMGA++ + N R+A GE
Sbjct: 237 AVPGDPSSAAFPLVAALIVPGSEVTVEGVMLNELRTGLFTTLQEMGADLVISNVRVASGE 296

Query: 300 DVADLRVRYSELKGVTVPEERAPSMIDEYPVLAVAAAFAEGATVMNGLDELRVKESDRLS 359
           +V D+  RYS+LKGV VP ERAPSMIDEYP+LAVAAAFA G TVM G+ E+RVKESDR+S
Sbjct: 297 EVGDITARYSQLKGVVVPPERAPSMIDEYPILAVAAAFASGETVMRGVGEMRVKESDRIS 356

Query: 360 AVADGLKLNGVDCDEGEASLVVRGRPGGKGLGNAAGGQVKTHLDHRIAMSFLVLGLASEH 419
             A+GLK  GV   E     +V     G G     G  V TH DHRIAMS L+LG+A++ 
Sbjct: 357 LTANGLKACGVQVVEEPEGFIVT----GTGQPPKGGATVVTHGDHRIAMSHLILGMAAQA 412

Query: 420 PVTVDDATMIATSFPEFMDLMTGLGATI 447
            V VD+  MIATSFP F DLM GLGAT+
Sbjct: 413 EVAVDEPGMIATSFPGFADLMRGLGATL 440


Lambda     K      H
   0.316    0.135    0.385 

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: 676
Number of extensions: 31
Number of successful extensions: 5
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: 448
Length of database: 443
Length adjustment: 32
Effective length of query: 416
Effective length of database: 411
Effective search space:   170976
Effective search space used:   170976
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: 41 (21.6 bits)
S2: 51 (24.3 bits)

Align candidate CCNA_03704 CCNA_03704 (3-phosphoshikimate 1-carboxyvinyltransferase)
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.30320.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.1e-128  413.3   0.0   5.8e-128  413.1   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_03704  CCNA_03704 3-phosphoshikimate 1-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_03704  CCNA_03704 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  413.1   0.0  5.8e-128  5.8e-128       1     414 [.      16     438 ..      16     439 .. 0.95

  Alignments for each domain:
  == domain 1  score: 413.1 bits;  conditional E-value: 5.8e-128
                             TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveee.keelviegvgglkepeae 72 
                                           g++++pg+KSishR+++l+aLa g+t+v++lL+++D+lat +a++++Ga++e+e  +++ ieg+gg++ep ++
  lcl|FitnessBrowser__Caulo:CCNA_03704  16 GIVRAPGDKSISHRSMILGALATGTTTVEGLLEGDDVLATARAMQAFGARIEREgVGRWRIEGKGGFEEPVDV 88 
                                           789*************************************************7769***************** PP

                             TIGR01356  73 ldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgplkggiv 145
                                           +d+gn+Gt +Rl++g++a  ++  ++tgd+sl+ RP++r++++L ++ga+   ++ +g+lPl+++g++  g  
  lcl|FitnessBrowser__Caulo:CCNA_03704  89 IDCGNAGTGVRLIMGAAAGFAMCATFTGDQSLRGRPMGRVLDPLARMGATWLGRD-KGRLPLTLKGGNLRGLN 160
                                           *****************************************************99.59********8888*** PP

                             TIGR01356 146 elsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeede....rkivvkggqk 214
                                           +  ++aS+Q+ksa+lla+   l+a++   v+e++ +r+++e++L  ++++ +  +++ +    r++++++gqk
  lcl|FitnessBrowser__Caulo:CCNA_03704 161 YTLPMASAQVKSAVLLAG---LHAEGGVEVIEPEATRDHTERMLRAFGAEVIVEDRKAGdktfRHVRLPEGQK 230
                                           ******************...55555555566****************9965444444367789999****** PP

                             TIGR01356 215 ykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadveveeqr........dv 278
                                            + ++v+v+gD+SsAaf+l+aa+i ++ evtve+++ n+++++  ++++L+emGad+ + + r        d+
  lcl|FitnessBrowser__Caulo:CCNA_03704 231 LTGTHVAVPGDPSSAAFPLVAALIVPGsEVTVEGVMLNELRTG--LFTTLQEMGADLVISNVRvasgeevgDI 301
                                           88899**********************9***************..888*************99999****999 PP

                             TIGR01356 279 evegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklGveveele 350
                                           + +  s+lkgv v +++++s+iDe+p+lav+aafA+get+++++ e+RvkEsdRi+ +a+ L++ Gv+v e +
  lcl|FitnessBrowser__Caulo:CCNA_03704 302 TAR-YSQLKGVVVpPERAPSMIDEYPILAVAAAFASGETVMRGVGEMRVKESDRISLTANGLKACGVQVVEEP 373
                                           999.789******99********************************************************** PP

                             TIGR01356 351 dgllieGkkkelkg.avvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfevleqlga 414
                                           +g++++G+ +  kg a+v t++DHRiam+  +lg+aa++ev +++++++a+sfP F ++++ lga
  lcl|FitnessBrowser__Caulo:CCNA_03704 374 EGFIVTGTGQPPKGgATVVTHGDHRIAMSHLILGMAAQAEVAVDEPGMIATSFPGFADLMRGLGA 438
                                           ********97777769********************************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (443 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.60
//
[ok]

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