Alignments for a candidate for aroA in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Pedobacter sp. GW460-11-11-14-LB5

Align 3-phosphoshikimate 1-carboxyvinyltransferase; EC 2.5.1.19 (characterized, see rationale)
to candidate CA265_RS11640 CA265_RS11640 3-phosphoshikimate 1-carboxyvinyltransferase

Query= uniprot:L0FR45
         (405 letters)



>FitnessBrowser__Pedo557:CA265_RS11640
          Length = 422

 Score =  342 bits (877), Expect = 1e-98
 Identities = 194/406 (47%), Positives = 259/406 (63%), Gaps = 25/406 (6%)

Query: 17  IPLPSSKSESNRVLIVDALTEGQNQISNLAEARDTQTMIRLL----------AEDPETLD 66
           I L  SKSE NR LI+ AL++   ++ NL+ A DT T+  +L           ++ +T+D
Sbjct: 19  IQLTGSKSECNRALIISALSKKLVKVENLSNAADTVTLNGILNNLEEELEVEIQESKTVD 78

Query: 67  VLDAGTTMRFLTAYAALTNRRKTLTGTPRMCERPIGILVDALRAIGAKIEYKGKEGYPPM 126
           V  AGT MRFL+AY +  N    LTGT RM +RPIGIL +AL+ IGA I Y   EG+PP+
Sbjct: 79  VGPAGTAMRFLSAYLSAKNGNFLLTGTERMKQRPIGILAEALKTIGADISYAEAEGFPPL 138

Query: 127 ETLGFEKQLTNKVQIRGDVSSQYISALLMNAPLLPEGLTLELTGKIGSKTYITMTLELMK 186
             +G   Q T +V+I+GD+SSQYISALLM AP+LP+GLTLE+ G++ SK Y+ MTL+++ 
Sbjct: 139 NIVGPLNQKTAEVKIKGDISSQYISALLMIAPILPQGLTLEIEGELTSKPYVDMTLDMLA 198

Query: 187 QFGIAYSFEGNTISIAPQSYKNTSFAVESDWSGASYWFSLLACADEGSFFLKGLKENSLQ 246
           + GIA+S+ GN+ISI PQ++K  +  VE DWS ASYW+S+ A ADE    L  LKE SLQ
Sbjct: 199 EVGIAHSWNGNSISIKPQAFKPGTLVVEPDWSAASYWYSIAALADEAEISLPALKEKSLQ 258

Query: 247 GDSKIVEIMDKLGVQSEFKDDGILLTKKAITGLG-------SYDFTHCPDLAQTVAVTCA 299
           GDS+I  IM   G+ +   D+GI     AI+ LG         D   CPDLAQT+ V  A
Sbjct: 259 GDSQIKNIMKIFGIATSKTDNGI-----AISNLGLSLDTKEVLDLKTCPDLAQTIVVIAA 313

Query: 300 LIGQKSQFTGLESLRIKETDRIYALQQELAKFNAKLEEGENGAFTV-IPSTDIPANVTIE 358
            +G+   FTGLE+L+IKETDRI ALQ ELAK    L E +N  +T+   +   P  +TI 
Sbjct: 314 ALGKNMAFTGLETLKIKETDRIAALQNELAKIGVTLTE-DNLVYTLNTDNLHFPDKITIA 372

Query: 359 TYDDHRMGMAFMPL-VTKTSVTLLDKEVVNKSYPSFWKHCVLAGIE 403
           TY+DHRM MAF PL +    V + + +VV KSYP +W+    AG +
Sbjct: 373 TYEDHRMAMAFAPLALLINEVEIEEMQVVEKSYPYYWEDLKKAGFD 418


Lambda     K      H
   0.316    0.133    0.376 

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: 386
Number of extensions: 18
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: 405
Length of database: 422
Length adjustment: 31
Effective length of query: 374
Effective length of database: 391
Effective search space:   146234
Effective search space used:   146234
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: 50 (23.9 bits)

Align candidate CA265_RS11640 CA265_RS11640 (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.27260.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
    2.6e-95  305.6   0.1    3.1e-95  305.4   0.1    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS11640  CA265_RS11640 3-phosphoshikimate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS11640  CA265_RS11640 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  305.4   0.1   3.1e-95   3.1e-95       2     412 ..      18     415 ..      17     418 .. 0.93

  Alignments for each domain:
  == domain 1  score: 305.4 bits;  conditional E-value: 3.1e-95
                                  TIGR01356   2 eikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveeekeelviegvgglkep 69 
                                                ei++ gsKS  +Ral+++aL+++ ++v+nl +++Dt +   +l++l  + e     + i++       
  lcl|FitnessBrowser__Pedo557:CA265_RS11640  18 EIQLTGSKSECNRALIISALSKKLVKVENLSNAADTVTLNGILNNLEEELE-----VEIQES------ 74 
                                                7999****************************************9987777.....666663...... PP

                                  TIGR01356  70 eaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlais 137
                                                 +++d+g +Gt++R+l++ l++ +g++ ltg e++k+RPi+ l eaL+ +ga+i+++e eg++Pl+i 
  lcl|FitnessBrowser__Pedo557:CA265_RS11640  75 -KTVDVGPAGTAMRFLSAYLSAKNGNFLLTGTERMKQRPIGILAEALKTIGADISYAEAEGFPPLNIV 141
                                                .58***************************************************************** PP

                                  TIGR01356 138 gp.lkg.givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeed 203
                                                gp ++  + v+++g++SsQy+sall+ ap   q+ tlei+g +l s+py+++tL++l++ g+  + + 
  lcl|FitnessBrowser__Pedo557:CA265_RS11640 142 GPlNQKtAEVKIKGDISSQYISALLMIAPILPQGLTLEIEG-ELTSKPYVDMTLDMLAEVGIAHSWNG 208
                                                **844459*********************************.*******************9999987 PP

                                  TIGR01356 204 erkivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadv 270
                                                + +i++k+++  k+ ++ ve D S+A+++  +aa++ e e+ +  l e+s+qgd +i ++++ +G   
  lcl|FitnessBrowser__Pedo557:CA265_RS11640 209 N-SISIKPQA-FKPGTLVVEPDWSAASYWYSIAALADEaEISLPALKEKSLQGDSQIKNIMKIFGIAT 274
                                                6.*****975.88889*************************************************998 PP

                                  TIGR01356 271 eveeqrdvevegasklkgvkv.d.idvdsliDelptlavlaafAegetriknieelRvkEsdRiaaia 336
                                                + +++  + + +  +l+ ++  +  d+++++D+++t+ v+aa    +   +++e+l++kE+dRiaa+ 
  lcl|FitnessBrowser__Pedo557:CA265_RS11640 275 SKTDN-GIAISN-LGLS-LDTkEvLDLKTCPDLAQTIVVIAAALGKNMAFTGLETLKIKETDRIAALQ 339
                                                88888.699996.3443.3332337****************99999999******************* PP

                                  TIGR01356 337 eeLeklGveveeledgllieGkk.kelkgavvdtydDHRiamalavlglaaegeveiedaecvaksfP 403
                                                +eL+k+Gv+ +e +   + +  + +   + ++ ty+DHR+ama+a l+l  + eveie+ ++v+ks+P
  lcl|FitnessBrowser__Pedo557:CA265_RS11640 340 NELAKIGVTLTEDNLVYTLNTDNlHFPDKITIATYEDHRMAMAFAPLALLIN-EVEIEEMQVVEKSYP 406
                                                ************999999999986666679*********************8.*************** PP

                                  TIGR01356 404 eFfevleql 412
                                                +++e+l++ 
  lcl|FitnessBrowser__Pedo557:CA265_RS11640 407 YYWEDLKKA 415
                                                *****9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (422 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.75
//
[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