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

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.23828.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  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592  3-isopropylmalate dehydratase la


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592  3-isopropylmalate dehydratase large subunit (EC 4.2.1.33)
   #    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.aenetdllyidrhlvhevtspqafeglraagrkvrrvd 55 
                                                             ++tly+k  d+h v   ++++  llyidr +  e tspqaf g+r+agrk  r++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592   4 PRTLYQKHIDSHTVCAlDDQGHVLLYIDRQVANEYTSPQAFSGMREAGRKAWRPG 58 
                                                             89**********987626677889******************************* PP

                                               TIGR00170  56 ktlatldhniste.srdveikeekaklqvkeleknvkefgvklfdlssaeqgivh 109
                                                              tla +dh  +t+ +r   + +    +qv  +e+n+++fg++lfd+ +++qgi h
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592  59 ATLAVVDHVNPTVpTRTAAMPDAGGARQVSYFEENCRDFGIELFDVLDKRQGIEH 113
                                                             ********999973566677788899***************************** PP

                                               TIGR00170 110 vvgpeegltlpgktivcgdshtathgafgalafgigtsevehvlatqtlkqarak 164
                                                             vv pe+g+ lpg+ +  gdsht+t+ga+ga+ fgigtse+eh+la+qtl+ +r k
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592 114 VVAPEQGFILPGMVVAAGDSHTTTYGALGAFGFGIGTSEIEHLLASQTLVYKRLK 168
                                                             ******************************************************* PP

                                               TIGR00170 165 tlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtv 219
                                                             t++++v+g l +g+t+kdii+a+i kig++g tgy +efag ai dls+e+rmt+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592 169 TMRVTVNGVLGTGVTSKDIIMALIEKIGASGATGYAIEFAGPAISDLSVEARMTI 223
                                                             ******************************************************* PP

                                               TIGR00170 220 cnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfd 274
                                                             cnma+eaga+  ++apd+  f+y+++++ ap+g+ +e+ava+w+ l++dega+fd
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592 224 CNMAVEAGARGAFMAPDDKVFAYLQHKPRAPQGQLWEQAVAKWRGLHSDEGAVFD 278
                                                             ******************************************************* PP

                                               TIGR00170 275 kvvtleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylgle 329
                                                             ++vtl+   + p+vtwgt+p+q+ sv ++vpdp+   d + ++++++al+y+gl+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592 279 REVTLDVAALEPMVTWGTSPDQAASVGGHVPDPAAQPDLILRQGMQRALNYMGLT 333
                                                             ******************************************************* PP

                                               TIGR00170 330 pgtklkdikvdkvfigsctnsriedlraaaevvkgkkvadnvklalvvpgsglvk 384
                                                             pg++l d+ + + figsctn+riedlr  a vv+gk+va+ v+ a++vpgs lv+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592 334 PGMPLSDVVISHAFIGSCTNARIEDLRDVARVVRGKRVASHVR-AMIVPGSTLVR 387
                                                             *******************************************.*********** PP

                                               TIGR00170 385 kqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgk 439
                                                             +qae egl +ifl+agfewr++gcs+cl+mn+dvl +++rcas++nrnfegrqg+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592 388 HQAEDEGLAQIFLDAGFEWRQSGCSMCLAMNDDVLAPGDRCASSTNRNFEGRQGA 442
                                                             ******************************************************* PP

                                               TIGR00170 440 garthlvspamaaaaavagkfvdirel 466
                                                             garthl+spam aaaa++g++ d+r +
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592 443 GARTHLMSPAMVAAAAITGHLTDVRTF 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 6.94
//
[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