Alignments for a candidate for trpE in Trichodesmium erythraeum IMS101

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Trichodesmium erythraeum IMS101

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate WP_011613168.1 TERY_RS18205 anthranilate synthase component I

Query= SwissProt::P20579
         (493 letters)



>NCBI__GCF_000014265.1:WP_011613168.1
          Length = 511

 Score =  400 bits (1029), Expect = e-116
 Identities = 232/501 (46%), Positives = 321/501 (64%), Gaps = 24/501 (4%)

Query: 5   EFLRLAAVGYNRIPLACETLADFDTPLSIYLKLA-DQPNSYLLESVQGGEKWGRYSMIGL 63
           EF RLA  G N +P+  E +AD DTP+S + ++  DQP S+LLESV+GGEK GRYS +G 
Sbjct: 8   EFSRLAKQG-NFVPVYQEWIADLDTPVSSWYRVCKDQPYSFLLESVEGGEKIGRYSFLGC 66

Query: 64  PSRTVMRVHGYHVSILHDGVEVESHDVEDPLAFVESFKDRYKVADIPGLPRFNGGLVGYF 123
               ++   G H +  +   +V++ +  +P   + +    YK   +P LP   GGL G++
Sbjct: 67  DPLWILEARGDHTTQTYRDGKVKTFE-GNPFDVLNNCLQDYKPVKLPQLPSGIGGLFGFW 125

Query: 124 GYDCVRYVEKRLGVSPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVDPAE-----E 178
           GY+ +R++E R+GV P  +   +PD L M  D ++VFD +  K+ AI   D        E
Sbjct: 126 GYELIRWIEPRVGVYPATEN-DLPDGLWMQVDNLLVFDQVKRKILAIAYADIRSPEANLE 184

Query: 179 QAFEQGQARLQGLLETLRQPITPRRGL-DLSGPQAAEPEFRSSYT----REDYENAVGRI 233
            A++Q   R+  L++ LR P++ +  L +   P+  + EF   +T    R  +   V + 
Sbjct: 185 LAYQQTCDRVSELVDKLRSPLSRQNTLLEWQPPEGKDKEFTDIHTSNTPRAKFCANVEKA 244

Query: 234 KEYILAGDCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVL 293
           KEYI AGD  QVV SQ++S ++   P  LYR+LR  NP+PYM +FNFG++ V+GSSPEV+
Sbjct: 245 KEYIKAGDIFQVVISQQLSTEYTGEPFALYRSLRLINPSPYMAYFNFGNWQVIGSSPEVM 304

Query: 294 VRVEDN-----LVTVRPIAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVG 348
           V+ E       L TVRPIAGTR RG T   D AL ++LL D KE AEH+ML+DLGRND+G
Sbjct: 305 VKAEKTPDGKRLATVRPIAGTRRRGKTYAEDNALAEELLQDPKERAEHIMLVDLGRNDLG 364

Query: 349 RVSSTGSVRLTEKMVIERYSNVMHIVSNVAGQLREGLTAMDALRAILPAGTLSGAPKIRA 408
           RV   G+V++ + MVIERYS+VMHIVSNV G+L +  TA D L+A  PAGT+SGAPKIRA
Sbjct: 365 RVCQVGTVKVDQLMVIERYSHVMHIVSNVVGELADDRTAWDLLKACFPAGTVSGAPKIRA 424

Query: 409 MEIIDELEPVKRGVYGGAVGYFAWNGNMDTAIAIRTAVI---NDG--ELHVQAGGGIVAD 463
           MEII+ELEP +RGVY G  GY+ + G +++AI IRT V+   N+G   + VQAG G+VAD
Sbjct: 425 MEIINELEPCRRGVYSGVYGYYDFEGQLNSAITIRTMVVRPKNNGTHTVTVQAGAGLVAD 484

Query: 464 SVPALEWEETINKRRAMFRAV 484
           SV   E+EETINK R +  A+
Sbjct: 485 SVAETEYEETINKARGLLEAI 505


Lambda     K      H
   0.320    0.138    0.403 

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: 641
Number of extensions: 34
Number of successful extensions: 7
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: 493
Length of database: 511
Length adjustment: 34
Effective length of query: 459
Effective length of database: 477
Effective search space:   218943
Effective search space used:   218943
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 (21.8 bits)
S2: 52 (24.6 bits)

Align candidate WP_011613168.1 TERY_RS18205 (anthranilate synthase component I)
to HMM TIGR00564 (trpE: anthranilate synthase component I (EC 4.1.3.27))

# 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/TIGR00564.hmm
# target sequence database:        /tmp/gapView.19858.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00564  [M=455]
Accession:   TIGR00564
Description: trpE_most: anthranilate synthase component I
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.2e-162  525.2   0.0   9.3e-162  525.0   0.0    1.0  1  lcl|NCBI__GCF_000014265.1:WP_011613168.1  TERY_RS18205 anthranilate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000014265.1:WP_011613168.1  TERY_RS18205 anthranilate synthase component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  525.0   0.0  9.3e-162  9.3e-162       2     454 ..      28     505 ..      27     506 .. 0.93

  Alignments for each domain:
  == domain 1  score: 525.0 bits;  conditional E-value: 9.3e-162
                                 TIGR00564   2 dtltpisvylklak.rkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeakieedel 69 
                                               d  tp+s   ++ k +++sfllEsve +e++gRyS++g++p   ++a+++++++   d++ ++ e+++ 
  lcl|NCBI__GCF_000014265.1:WP_011613168.1  28 DLDTPVSSWYRVCKdQPYSFLLESVEGGEKIGRYSFLGCDPLWILEARGDHTTQTYRDGKVKTFEGNPF 96 
                                               6789999999998879**********************************9999999999999****** PP

                                 TIGR00564  70 kelrklleka.eesedeldeplsggavGylgydtvrlveklkeea.edelelpdlllllvetvivfDhv 136
                                               ++l+++l+ +   + ++l+    gg++G+ gy+++r +e+        e +lpd l + v++++vfD+v
  lcl|NCBI__GCF_000014265.1:WP_011613168.1  97 DVLNNCLQDYkPVKLPQLPS-GIGGLFGFWGYELIRWIEPRVGVYpATENDLPDGLWMQVDNLLVFDQV 164
                                               *********97788888887.579***************99986659999******************* PP

                                 TIGR00564 137 ekkvilienarteaers....aeeeaaarleellaelqkelekavkaleekkes.........ftsnve 192
                                               ++k++ i++a  ++ +     a++++ +r++el+ +l+++l+++++ le ++ +          tsn+ 
  lcl|NCBI__GCF_000014265.1:WP_011613168.1 165 KRKILAIAYADIRSPEAnlelAYQQTCDRVSELVDKLRSPLSRQNTLLEWQPPEgkdkeftdiHTSNTP 233
                                               ********99888776678899999***************99985554444433444677777778888 PP

                                 TIGR00564 193 keeyeekvakakeyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPE 261
                                               ++++ ++v+kakeyikaGdifqvv+Sq+l+++ + +pf+lYr+LR +NPSpy++y+++ + +++gsSPE
  lcl|NCBI__GCF_000014265.1:WP_011613168.1 234 RAKFCANVEKAKEYIKAGDIFQVVISQQLSTEYTGEPFALYRSLRLINPSPYMAYFNFGNWQVIGSSPE 302
                                               8******************************************************************** PP

                                 TIGR00564 262 llvkvk....gkr.vetrPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgs 325
                                               ++vk +    gkr  ++rPiAGtr+RG+t +eD+al+eeLl+d+KerAEH+mLvDL+RND+g+v+++g+
  lcl|NCBI__GCF_000014265.1:WP_011613168.1 303 VMVKAEktpdGKRlATVRPIAGTRRRGKTYAEDNALAEELLQDPKERAEHIMLVDLGRNDLGRVCQVGT 371
                                               ****998898788899***************************************************** PP

                                 TIGR00564 326 vevkellkiekyshvmHivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmelidelEkekRgiYg 394
                                               v+v++l+ ie+yshvmHivS+V+Gel+d+ ta+D l+a++PaGT+sGAPK+rAme+i+elE+ +Rg+Y+
  lcl|NCBI__GCF_000014265.1:WP_011613168.1 372 VKVDQLMVIERYSHVMHIVSNVVGELADDRTAWDLLKACFPAGTVSGAPKIRAMEIINELEPCRRGVYS 440
                                               ********************************************************************* PP

                                 TIGR00564 395 GavgylsfdgdvdtaiaiRtmvl.....kdgvayvqAgaGiVaDSdpeaEyeEtlnKakallrai 454
                                               G+ gy++f+g++++ai+iRtmv+       +++ vqAgaG+VaDS+ e+EyeEt+nKa++ll+ai
  lcl|NCBI__GCF_000014265.1:WP_011613168.1 441 GVYGYYDFEGQLNSAITIRTMVVrpknnGTHTVTVQAGAGLVADSVAETEYEETINKARGLLEAI 505
                                               ***********************44322235789***************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (511 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 7.64
//
[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