Alignments for a candidate for aroA in Crocosphaera subtropica ATCC 51142

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Crocosphaera subtropica ATCC 51142

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_009545595.1 CCE_RS08425 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::K9TX81
         (448 letters)



>NCBI__GCF_000017845.1:WP_009545595.1
          Length = 451

 Score =  671 bits (1730), Expect = 0.0
 Identities = 338/447 (75%), Positives = 390/447 (87%)

Query: 1   MLASPFAVETIDRQQNLIVTRPQTGFCLRGRIRIPGDKSISHRALMLGALANGETQIQGL 60
           M  S   +++++ QQ L +T P TG  L+G ++IPGDKSISHRALMLGA+A GET I GL
Sbjct: 1   MSKSIINLQSVENQQILSITPPNTGLSLQGTLQIPGDKSISHRALMLGAIAEGETIIAGL 60

Query: 61  LLGEDPRSTASCFRAMGAEISELNTDLVRVKGIGLGQLQEPADVLDAGNSGTTIRLMLGI 120
           LLGEDPRSTA CFRAMGA+IS LN++ V ++GIGLG+LQEP DVL+AGNSGTT+RLMLG+
Sbjct: 61  LLGEDPRSTAECFRAMGAQISPLNSEKVTIQGIGLGKLQEPLDVLNAGNSGTTMRLMLGL 120

Query: 121 LASHPERFFTVTGDSSLRSRPMSRVVKPLQQMEAQIWGRKGNSLAPLAIQGQNLKPIHYQ 180
           LASHP+R F VTGD+SLRSRPMSRV++PLQ M A IWGRK N+LAPLA+QG++LKPIHY 
Sbjct: 121 LASHPDRLFCVTGDASLRSRPMSRVIQPLQDMGANIWGRKNNTLAPLAVQGKSLKPIHYH 180

Query: 181 SPIASAQVKSCILLAGLMTEGKTTVTEPALSRDHSERMLQAFGAQLSVDPQTHSVTVTGP 240
           SPIASAQVKSCILLAGLMT+GKTTVTEPALSRDHSERMLQAFGA L +D QT+SVT+ G 
Sbjct: 181 SPIASAQVKSCILLAGLMTDGKTTVTEPALSRDHSERMLQAFGATLDIDSQTNSVTINGH 240

Query: 241 AQLQGQQVVVPGDISSAAFWLVAGAIVPDSELVIENVGVNPTRTGILAALEMMGADIQLE 300
            +L GQ V+VPGDISS+AFWLVA +IVP SEL+IENVG+NPTRTGIL ALEMMGADI LE
Sbjct: 241 PKLIGQTVIVPGDISSSAFWLVAASIVPGSELLIENVGINPTRTGILEALEMMGADITLE 300

Query: 301 NQRVVAGEPVADLRVRSGGLKACTIAGDLIPRLIDEIPILAVAAVFASGTTIIRDAAELR 360
           N+R++ GEPVADLRV+S  LK CTI G++IPRLIDE+PILAVA +FA+G TII+DAAELR
Sbjct: 301 NKRILTGEPVADLRVKSCQLKGCTIGGNIIPRLIDEVPILAVAGIFATGKTIIKDAAELR 360

Query: 361 VKESDRLAAMATELNRMGAKVTELPDGLEITGGTALKGTEVDSYTDHRIAMSLAIAALNA 420
           VKESDRLA MA+EL +MGAK+TELPDGLEITGGT LK  EVDSYTDHRIAMSLAIAALNA
Sbjct: 361 VKESDRLAVMASELTKMGAKITELPDGLEITGGTPLKAAEVDSYTDHRIAMSLAIAALNA 420

Query: 421 SGTTTISRAEAAAISYPDFIPTLQQVC 447
            G T I+RAEAAAISYP F+ TLQQVC
Sbjct: 421 KGKTIINRAEAAAISYPKFVETLQQVC 447


Lambda     K      H
   0.318    0.133    0.372 

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: 699
Number of extensions: 21
Number of successful extensions: 2
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: 451
Length adjustment: 33
Effective length of query: 415
Effective length of database: 418
Effective search space:   173470
Effective search space used:   173470
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_009545595.1 CCE_RS08425 (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.13221.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.9e-132  426.6   0.3   5.6e-132  426.4   0.3    1.0  1  lcl|NCBI__GCF_000017845.1:WP_009545595.1  CCE_RS08425 3-phosphoshikimate 1


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017845.1:WP_009545595.1  CCE_RS08425 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  426.4   0.3  5.6e-132  5.6e-132       1     413 [.      30     447 ..      30     449 .. 0.96

  Alignments for each domain:
  == domain 1  score: 426.4 bits;  conditional E-value: 5.6e-132
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.eekeelviegvgg..l 66 
                                               g ++ipg+KSishRal+l+a+aeget++ +lL +eD ++t e++r++Ga+++  + e+++i+g+g   l
  lcl|NCBI__GCF_000017845.1:WP_009545595.1  30 GTLQIPGDKSISHRALMLGAIAEGETIIAGLLLGEDPRSTAECFRAMGAQISpLNSEKVTIQGIGLgkL 98 
                                               6799************************************************888********998889 PP

                                 TIGR01356  67 kepeaeldlgnsGttaRlltgvlalas.gevvltgdeslkkRPierlveaLrelgaeieskeeegslPl 134
                                               +ep ++l++gnsGtt+Rl++g+la ++   + +tgd sl+ RP+ r++++L+ +ga+i  ++++  +Pl
  lcl|NCBI__GCF_000017845.1:WP_009545595.1  99 QEPLDVLNAGNSGTTMRLMLGLLASHPdRLFCVTGDASLRSRPMSRVIQPLQDMGANIWGRKNNTLAPL 167
                                               9999********************9999999************************************** PP

                                 TIGR01356 135 aisgplkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeed 203
                                               a++g++  +i++ s+ aS+Q+ks++lla+   l +++ ++v+e+ +sr++ e++L+ +++   +++ ++
  lcl|NCBI__GCF_000017845.1:WP_009545595.1 168 AVQGKSLKPIHYHSPIASAQVKSCILLAG---LMTDGKTTVTEPALSRDHSERMLQAFGAT-LDIDSQT 232
                                               ****7666*********************...66788899999****************88.8998887 PP

                                 TIGR01356 204 erkivvkggqk.ykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadv 270
                                               + +++++g+ k ++q+ v v+gD+Ss af+l+aa i ++ e+ +en+g+n+t+++  i++ Le mGad+
  lcl|NCBI__GCF_000017845.1:WP_009545595.1 233 N-SVTINGHPKlIGQT-VIVPGDISSSAFWLVAASIVPGsELLIENVGINPTRTG--ILEALEMMGADI 297
                                               6.*********66666.********************999***************..889********* PP

                                 TIGR01356 271 eveeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsd 330
                                               ++e++r        d++v+ + +lkg ++    +++liDe+p+lav++ fA g+t ik+++elRvkEsd
  lcl|NCBI__GCF_000017845.1:WP_009545595.1 298 TLENKRiltgepvaDLRVK-SCQLKGCTIgGNIIPRLIDEVPILAVAGIFATGKTIIKDAAELRVKESD 365
                                               *******************.689******99************************************** PP

                                 TIGR01356 331 RiaaiaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecva 399
                                               R+a++a+eL+k+G++++el+dgl+i+G+ + lk a+vd+y DHRiam+la+++l a+g+++i++ae++a
  lcl|NCBI__GCF_000017845.1:WP_009545595.1 366 RLAVMASELTKMGAKITELPDGLEITGG-TPLKAAEVDSYTDHRIAMSLAIAALNAKGKTIINRAEAAA 433
                                               ****************************.6*************************************** PP

                                 TIGR01356 400 ksfPeFfevleqlg 413
                                               +s+P+F+e l+q+ 
  lcl|NCBI__GCF_000017845.1:WP_009545595.1 434 ISYPKFVETLQQVC 447
                                               **********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (451 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: 00:00:00.01
# Mc/sec: 12.27
//
[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