Alignments for a candidate for trpE in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Azospirillum brasilense Sp245

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate AZOBR_RS07490 AZOBR_RS07490 anthranilate synthase subunit I

Query= SwissProt::P20579
         (493 letters)



>FitnessBrowser__azobra:AZOBR_RS07490
          Length = 503

 Score =  399 bits (1025), Expect = e-115
 Identities = 235/485 (48%), Positives = 307/485 (63%), Gaps = 33/485 (6%)

Query: 24  LADFDTPLSIYLKLAD-QPNSYLLESVQ--GGEKWGRYSMIGLPSRTVMRVHGYHVSI-- 78
           ++D +TP+S Y+KLAD +P  +L ES +   G +  RYS+IG     V R       +  
Sbjct: 27  VSDLETPVSAYMKLADGRPFGFLFESAERGAGSRRDRYSVIGFKPDLVWRCRRDRAEVNR 86

Query: 79  --LHDGVEVESHDVEDPLAFVESFKDRYKVADIP-GLPRFNGGLVGYFGYDCVRYVEKRL 135
             LHD    E  D   PL  + +  +  ++ D+P  LP    GL GY  YD VR +E+  
Sbjct: 87  NALHDRDAYEPIDAA-PLESLRALINESRI-DLPDALPPMAAGLFGYLTYDMVRLMERL- 143

Query: 136 GVSPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVDPAE----EQAFEQGQARLQGL 191
               NPD LG+PD +L     V +FD+    +  +  V P        A+   + RL   
Sbjct: 144 -PDDNPDELGIPDAILSRPSIVAIFDSHTDSVTLVTPVWPKPGVDGAAAYGDARERLMDA 202

Query: 192 LETLRQPITPRR------GLDLSGPQAAEPEFRSSYTREDYENAVGRIKEYILAGDCMQV 245
           +  L +P+  RR      GL L+        + S+ TRE+Y   V R KEYI AGD  QV
Sbjct: 203 VADLERPLPYRREPRTKDGLPLA--------WTSNTTREEYHAIVERAKEYIRAGDIFQV 254

Query: 246 VPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDNLVTVRP 305
           VPSQR+   FK +P+ LYR LR  NP+P+++  +FG+  VVGSSPE+LVRV D  VTVRP
Sbjct: 255 VPSQRIRFPFKPSPLALYRTLRRLNPSPFLFHCDFGELSVVGSSPEILVRVRDGNVTVRP 314

Query: 306 IAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVGRVSSTGSVRLTEKMVIE 365
           IAGTR RGAT   D+AL +DLLSD KE+AEHLML+DLGRNDVGRV+ TG+V++T+KM++E
Sbjct: 315 IAGTRKRGATAAEDQALAEDLLSDPKELAEHLMLLDLGRNDVGRVARTGTVKVTQKMIVE 374

Query: 366 RYSNVMHIVSNVAGQLREGLTAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKRGVYGG 425
            YS+VMHIVSNV G L     A+DAL A  PAGT+SGAPK+RAM+IIDELE  +RGVY G
Sbjct: 375 LYSHVMHIVSNVEGDLDPKHDALDALIAGFPAGTVSGAPKVRAMQIIDELEKARRGVYAG 434

Query: 426 AVGYFAWNGNMDTAIAIRTAVINDGELHVQAGGGIVADSVPALEWEETINKRRAMFRAVA 485
            VGYF  +G MDT IA+RTAV+ DG ++VQAGGG+VADS P  E++ET+NK  A+ RA  
Sbjct: 435 CVGYFGASGAMDTCIALRTAVLKDGMMYVQAGGGVVADSDPEAEYQETVNKSMALIRA-- 492

Query: 486 LAEQT 490
            AE+T
Sbjct: 493 -AEET 496


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: 718
Number of extensions: 30
Number of successful extensions: 4
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: 503
Length adjustment: 34
Effective length of query: 459
Effective length of database: 469
Effective search space:   215271
Effective search space used:   215271
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 AZOBR_RS07490 AZOBR_RS07490 (anthranilate synthase subunit 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.4308.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.6e-175  569.7   0.0     3e-175  569.5   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS07490  AZOBR_RS07490 anthranilate synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS07490  AZOBR_RS07490 anthranilate synthase subunit I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  569.5   0.0    3e-175    3e-175       2     454 ..      29     493 ..      28     494 .. 0.94

  Alignments for each domain:
  == domain 1  score: 569.5 bits;  conditional E-value: 3e-175
                                 TIGR00564   2 dtltpisvylklak.rkesfllEsvekee..elgRySliglnpvleikakdgkavlleaddeeak.... 63 
                                               d +tp+s+y kla  r+  fl+Es+e+++  +++RyS+ig +p+l+++++ ++a+  +++ ++      
  lcl|FitnessBrowser__azobra:AZOBR_RS07490  29 DLETPVSAYMKLADgRPFGFLFESAERGAgsRRDRYSVIGFKPDLVWRCRRDRAEVNRNALHDRDayep 97 
                                               889***********99**********9876699*****************9955444333322223367 PP

                                 TIGR00564  64 ieedelkelrkllekaeesedeldeplsggavGylgydtvrlveklkeeaedelelpdlllllvetviv 132
                                               i++++l++lr+l+++ +++ ++  +p+++g++Gyl+yd+vrl+e+l++ ++del +pd++l   + v++
  lcl|FitnessBrowser__azobra:AZOBR_RS07490  98 IDAAPLESLRALINESRIDLPDALPPMAAGLFGYLTYDMVRLMERLPDDNPDELGIPDAILSRPSIVAI 166
                                               9**************9888888889******************************************** PP

                                 TIGR00564 133 fDhvekkvilienarteaers...aeeeaaarleellaelqkelekavkaleekkes..ftsnvekeey 196
                                               fD  +++v+l++ +  + +++   a+ +a++rl + +a+l+++l  + +  +++  +   tsn+++eey
  lcl|FitnessBrowser__azobra:AZOBR_RS07490 167 FDSHTDSVTLVTPVWPKPGVDgaaAYGDARERLMDAVADLERPLPYRREPRTKDGLPlaWTSNTTREEY 235
                                               **************9999999888999****************986533333332224599******** PP

                                 TIGR00564 197 eekvakakeyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvk 265
                                               ++ v++akeyi+aGdifqvv+Sqr++ +++ +p++lYr+LR+ NPSp+l++ d+ ++++vgsSPE+lv+
  lcl|FitnessBrowser__azobra:AZOBR_RS07490 236 HAIVERAKEYIRAGDIFQVVPSQRIRFPFKPSPLALYRTLRRLNPSPFLFHCDFGELSVVGSSPEILVR 304
                                               ********************************************************************* PP

                                 TIGR00564 266 vkgkrvetrPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellki 334
                                               v++ +v++rPiAGtrkRGat +eD+al+e+Ll+d+Ke AEHlmL+DL+RND+g+va++g+v+v++ + +
  lcl|FitnessBrowser__azobra:AZOBR_RS07490 305 VRDGNVTVRPIAGTRKRGATAAEDQALAEDLLSDPKELAEHLMLLDLGRNDVGRVARTGTVKVTQKMIV 373
                                               ********************************************************************* PP

                                 TIGR00564 335 ekyshvmHivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfd 403
                                               e yshvmHivS+VeG l ++ +a+Dal+a +PaGT+sGAPKvrAm++idelEk +Rg+Y+G+vgy+++ 
  lcl|FitnessBrowser__azobra:AZOBR_RS07490 374 ELYSHVMHIVSNVEGDLDPKHDALDALIAGFPAGTVSGAPKVRAMQIIDELEKARRGVYAGCVGYFGAS 442
                                               ********************************************************************* PP

                                 TIGR00564 404 gdvdtaiaiRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKakallrai 454
                                               g++dt+ia+Rt+vlkdg++yvqAg+G+VaDSdpeaEy+Et+nK++al ra+
  lcl|FitnessBrowser__azobra:AZOBR_RS07490 443 GAMDTCIALRTAVLKDGMMYVQAGGGVVADSDPEAEYQETVNKSMALIRAA 493
                                               ***********************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (503 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: 00:00:00.09
# Mc/sec: 2.54
//
[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