GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Pseudomonas fluorescens GW456-L13

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate PfGW456L13_3592 3-isopropylmalate dehydratase large subunit (EC 4.2.1.33)

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592
          Length = 473

 Score =  507 bits (1306), Expect = e-148
 Identities = 248/465 (53%), Positives = 331/465 (71%), Gaps = 6/465 (1%)

Query: 3   KTLYEKLFDAHVVYEAENETP-LLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATM 61
           +TLY+K  D+H V   +++   LLYIDR + +E TSPQAF G+R  GR   +PG T A +
Sbjct: 5   RTLYQKHIDSHTVCALDDQGHVLLYIDRQVANEYTSPQAFSGMREAGRKAWRPGATLAVV 64

Query: 62  DH---NVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVT 118
           DH    V T+T  +   G   ++   E  +NC++FG+EL+D+    QGI HV+ PEQG  
Sbjct: 65  DHVNPTVPTRTAAMPDAGGARQVSYFE--ENCRDFGIELFDVLDKRQGIEHVVAPEQGFI 122

Query: 119 LPGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGI 178
           LPGM +  GDSHT T+GA GA  FGIGTSE+EH+LA+QTL   R KTM++ V G    G+
Sbjct: 123 LPGMVVAAGDSHTTTYGALGAFGFGIGTSEIEHLLASQTLVYKRLKTMRVTVNGVLGTGV 182

Query: 179 TAKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDET 238
           T+KDI++A+I K G++G TG+ +EF G AI DLS+E RMT+CNMA+E GA+   +APD+ 
Sbjct: 183 TSKDIIMALIEKIGASGATGYAIEFAGPAISDLSVEARMTICNMAVEAGARGAFMAPDDK 242

Query: 239 TFNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVI 298
            F Y++ +  AP+G+ ++ AVA W+ L +DEGA FD  VTL    + P VTWGT+P Q  
Sbjct: 243 VFAYLQHKPRAPQGQLWEQAVAKWRGLHSDEGAVFDREVTLDVAALEPMVTWGTSPDQAA 302

Query: 299 SVNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAA 358
           SV  ++PDPA+  D + R   ++AL YMGL PG+PL++V I   FIGSCTN+RIEDLR  
Sbjct: 303 SVGGHVPDPAAQPDLILRQGMQRALNYMGLTPGMPLSDVVISHAFIGSCTNARIEDLRDV 362

Query: 359 AEIAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRL 418
           A + +G++VA  V+A++VPGS  V+ QAE EGL +IF++AGFEWR  GCSMCLAMN+D L
Sbjct: 363 ARVVRGKRVASHVRAMIVPGSTLVRHQAEDEGLAQIFLDAGFEWRQSGCSMCLAMNDDVL 422

Query: 419 NPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIR 463
            PG+RCAS++NRNFEGRQG G RTHL+SPAM AAAA+TGH  D+R
Sbjct: 423 APGDRCASSTNRNFEGRQGAGARTHLMSPAMVAAAAITGHLTDVR 467


Lambda     K      H
   0.317    0.134    0.396 

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: 694
Number of extensions: 29
Number of successful extensions: 3
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: 466
Length of database: 473
Length adjustment: 33
Effective length of query: 433
Effective length of database: 440
Effective search space:   190520
Effective search space used:   190520
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 PfGW456L13_3592 (3-isopropylmalate dehydratase large subunit (EC 4.2.1.33))
to HMM TIGR00170 (leuC: 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33))

# 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/TIGR00170.hmm
# target sequence database:        /tmp/gapView.3035580.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00170  [M=466]
Accession:   TIGR00170
Description: leuC: 3-isopropylmalate dehydratase, large subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                           -----------
   7.4e-199  647.0   0.0   8.5e-199  646.8   0.0    1.0  1  FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  646.8   0.0  8.5e-199  8.5e-199       2     466 .]       4     469 ..       3     469 .. 0.98

  Alignments for each domain:
  == domain 1  score: 646.8 bits;  conditional E-value: 8.5e-199
                                           TIGR00170   2 aktlyeklfdahvvke.aenetdllyidrhlvhevtspqafeglraagrkvrrvdktla 59 
                                                         ++tly+k  d+h v   ++++  llyidr +  e tspqaf g+r+agrk  r++ tla
  FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592   4 PRTLYQKHIDSHTVCAlDDQGHVLLYIDRQVANEYTSPQAFSGMREAGRKAWRPGATLA 62 
                                                         89**********987626677889*********************************** PP

                                           TIGR00170  60 tldhniste.srdveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegl 117
                                                          +dh  +t+ +r   + +    +qv  +e+n+++fg++lfd+ +++qgi hvv pe+g+
  FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592  63 VVDHVNPTVpTRTAAMPDAGGARQVSYFEENCRDFGIELFDVLDKRQGIEHVVAPEQGF 121
                                                         ****999973566677788899************************************* PP

                                           TIGR00170 118 tlpgktivcgdshtathgafgalafgigtsevehvlatqtlkqaraktlkievegklak 176
                                                          lpg+ +  gdsht+t+ga+ga+ fgigtse+eh+la+qtl+ +r kt++++v+g l +
  FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592 122 ILPGMVVAAGDSHTTTYGALGAFGFGIGTSEIEHLLASQTLVYKRLKTMRVTVNGVLGT 180
                                                         *********************************************************** PP

                                           TIGR00170 177 gitakdiilaiigkigvaggtgyvvefageairdlsmeermtvcnmaieagakagliap 235
                                                         g+t+kdii+a+i kig++g tgy +efag ai dls+e+rmt+cnma+eaga+  ++ap
  FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592 181 GVTSKDIIMALIEKIGASGATGYAIEFAGPAISDLSVEARMTICNMAVEAGARGAFMAP 239
                                                         *********************************************************** PP

                                           TIGR00170 236 dettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtnp 294
                                                         d+  f+y+++++ ap+g+ +e+ava+w+ l++dega+fd++vtl+   + p+vtwgt+p
  FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592 240 DDKVFAYLQHKPRAPQGQLWEQAVAKWRGLHSDEGAVFDREVTLDVAALEPMVTWGTSP 298
                                                         *********************************************************** PP

                                           TIGR00170 295 gqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsrie 353
                                                         +q+ sv ++vpdp+   d + ++++++al+y+gl+pg++l d+ + + figsctn+rie
  FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592 299 DQAASVGGHVPDPAAQPDLILRQGMQRALNYMGLTPGMPLSDVVISHAFIGSCTNARIE 357
                                                         *********************************************************** PP

                                           TIGR00170 354 dlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslcl 412
                                                         dlr  a vv+gk+va+ v+ a++vpgs lv++qae egl +ifl+agfewr++gcs+cl
  FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592 358 DLRDVARVVRGKRVASHVR-AMIVPGSTLVRHQAEDEGLAQIFLDAGFEWRQSGCSMCL 415
                                                         *******************.*************************************** PP

                                           TIGR00170 413 gmnndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdirel 466
                                                         +mn+dvl +++rcas++nrnfegrqg+garthl+spam aaaa++g++ d+r +
  FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592 416 AMNDDVLAPGDRCASSTNRNFEGRQGAGARTHLMSPAMVAAAAITGHLTDVRTF 469
                                                         ****************************************************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (473 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: 13.97
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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:

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:

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:

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:

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