Alignments for a candidate for aroA in Thiomicrorhabdus arctica DSM 13458

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Thiomicrorhabdus arctica DSM 13458

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_019556283.1 F612_RS0103080 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::Q83E11
         (438 letters)



>NCBI__GCF_000381085.1:WP_019556283.1
          Length = 447

 Score =  436 bits (1122), Expect = e-127
 Identities = 231/441 (52%), Positives = 305/441 (69%), Gaps = 11/441 (2%)

Query: 3   YQTIPSQGLSGEICVPGDKSISHRAVLLAAIAEGQTQVDGFLMGADNLAMVSALQQMGAS 62
           ++  P   + G I VPGDKSISHR+++L AI+EG T V GFL G D+LA + A Q+MG  
Sbjct: 6   FKVQPGGTIKGRIRVPGDKSISHRSIMLGAISEGATTVTGFLEGDDSLATLKAFQEMGVQ 65

Query: 63  IQVIEDENILVVEGVGMTGLQAPPEALDCGNSGTAIRLLSGLLAGQPFNTVLTGDSSLQR 122
           I+     N+  ++GVG+ GL+ P + LD GNSGTA+RL++G+LAGQ F+  L GD+SL +
Sbjct: 66  IEGPNKGNV-TIQGVGLKGLKKPNKPLDMGNSGTAMRLMAGILAGQDFDCELIGDASLSK 124

Query: 123 RPMKRIIDPLTLMGAKIDST-GNVPPLKIYG--NPRLTGIHYQLPMASAQVKSCLLLAGL 179
           RPMKR+ DPL  MGA+I++  G +PPLKI G  +  LT I Y LPMASAQVKSC+LLAGL
Sbjct: 125 RPMKRVTDPLRAMGAQIETAEGGMPPLKITGTGDGSLTAIDYVLPMASAQVKSCVLLAGL 184

Query: 180 YARGKTCITEPAPSRDHTERLLKHFHYTLQKDK-----QSICVSGGGKLKANDISIPGDI 234
           YA+G+TC  EPAP+RDHTER+L  F Y +  +K        C+ GGGKL    I +P DI
Sbjct: 185 YAKGRTCALEPAPTRDHTERMLNGFGYEVISEKIDSQQMKACLMGGGKLTGRHIDVPSDI 244

Query: 235 SSAAFFIVAATITPGSAIRLCRVGVNPTRLGVINLLKMMGADIEVTHYTEKNEEPTADIT 294
           SSAAFF+ AA ++  S + +  VG+NPTR+G++N+L++MGADI + +  E   EP AD+ 
Sbjct: 245 SSAAFFMAAAAVSKDSDLVIEHVGMNPTRVGIVNILQLMGADITLENAHEVGGEPVADVH 304

Query: 295 VRHARLKGIDIPPDQVPLTIDEFPVLLIAAAVAQGKTVLRDAAELRVKETDRIAAMVDGL 354
           VR+A LKGI+IP + V L IDEFPVL + AA A GKTVL  A ELRVKE+DRI  M D L
Sbjct: 305 VRYAPLKGINIPKELVALAIDEFPVLFVVAASASGKTVLTGAEELRVKESDRIQVMADAL 364

Query: 355 QKLGIAAESLPDGVIIQGG--TLEGGEVNSYDDHRIAMAFAVAGTLAKGPVRIRNCDNVK 412
           Q +G+ A    DG++I GG  T +   + S+ DHRI+MA  +AG  A   + I +C NV 
Sbjct: 365 QAVGVDALPTEDGMVINGGIQTKQSAVIQSHHDHRISMAMTIAGLNAVSEIVIDDCANVN 424

Query: 413 TSFPNFVELANEVGMNVKGVR 433
           TSFP F+EL N+VGM V+ V+
Sbjct: 425 TSFPTFLELINQVGMQVEAVK 445


Lambda     K      H
   0.318    0.137    0.392 

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: 614
Number of extensions: 28
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: 438
Length of database: 447
Length adjustment: 32
Effective length of query: 406
Effective length of database: 415
Effective search space:   168490
Effective search space used:   168490
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_019556283.1 F612_RS0103080 (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.24073.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.3e-130  420.6   1.0   3.7e-130  420.4   1.0    1.0  1  lcl|NCBI__GCF_000381085.1:WP_019556283.1  F612_RS0103080 3-phosphoshikimat


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000381085.1:WP_019556283.1  F612_RS0103080 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  420.4   1.0  3.7e-130  3.7e-130       1     414 [.      16     439 ..      16     440 .. 0.95

  Alignments for each domain:
  == domain 1  score: 420.4 bits;  conditional E-value: 3.7e-130
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.eekeelviegvgg..l 66 
                                               g+i++pg+KSishR+++l+a++eg t+vt++L+++D latl+a++++G+++e  +k++++i+gvg   l
  lcl|NCBI__GCF_000381085.1:WP_019556283.1  16 GRIRVPGDKSISHRSIMLGAISEGATTVTGFLEGDDSLATLKAFQEMGVQIEgPNKGNVTIQGVGLkgL 84 
                                               79**************************************************7669*******99888* PP

                                 TIGR01356  67 kepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPla 135
                                               k p++ ld+gnsGt++Rl+ g+la ++++++l gd sl+kRP++r++++Lr++ga+ie +e  g +Pl+
  lcl|NCBI__GCF_000381085.1:WP_019556283.1  85 KKPNKPLDMGNSGTAMRLMAGILAGQDFDCELIGDASLSKRPMKRVTDPLRAMGAQIETAE-GGMPPLK 152
                                               **********************************************************988.69***** PP

                                 TIGR01356 136 isgp..lkg.givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgvevee 201
                                               i+g+   ++ +i ++ ++aS+Q+ks++lla+   l a++ +   e+  +r+++e++L+ ++ + ++ + 
  lcl|NCBI__GCF_000381085.1:WP_019556283.1 153 ITGTgdGSLtAIDYVLPMASAQVKSCVLLAG---LYAKGRTCALEPAPTRDHTERMLNGFGYEVISEKI 218
                                               ***98856679********************...667789999999*****************998777 PP

                                 TIGR01356 202 ede.rkivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGa 268
                                               + +  k  + gg+k + ++++v++D+SsAaff+aaaa+++  ++++e++g+n+t+ +  i+++L+ mGa
  lcl|NCBI__GCF_000381085.1:WP_019556283.1 219 DSQqMKACLMGGGKLTGRHIDVPSDISSAAFFMAAAAVSKDsDLVIEHVGMNPTRVG--IVNILQLMGA 285
                                               6665677788888888889*********************99***************..999******* PP

                                 TIGR01356 269 dveveeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkE 328
                                               d+++e+ +        dv v+    lkg+++ ++ v+ +iDe+p+l v+aa A+g+t+++++eelRvkE
  lcl|NCBI__GCF_000381085.1:WP_019556283.1 286 DITLENAHevggepvaDVHVR-YAPLKGINIpKELVALAIDEFPVLFVVAASASGKTVLTGAEELRVKE 353
                                               *******99************.568******88************************************ PP

                                 TIGR01356 329 sdRiaaiaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaec 397
                                               sdRi+++a++L+++Gv++ ++edg++i+G+ ++ ++av+++++DHRi ma++++gl a +e+ i+d + 
  lcl|NCBI__GCF_000381085.1:WP_019556283.1 354 SDRIQVMADALQAVGVDALPTEDGMVINGGIQTKQSAVIQSHHDHRISMAMTIAGLNAVSEIVIDDCAN 422
                                               ******************************877788********************************* PP

                                 TIGR01356 398 vaksfPeFfevleqlga 414
                                               v++sfP F+e+++q+g+
  lcl|NCBI__GCF_000381085.1:WP_019556283.1 423 VNTSFPTFLELINQVGM 439
                                               *************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (447 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: 00:00:00.01
# Mc/sec: 11.45
//
[ok]

This GapMind analysis is from Apr 10 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