Alignments for a candidate for hutU in Bacteroides thetaiotaomicron VPI-5482

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutU in Bacteroides thetaiotaomicron VPI-5482

Align Urocanate hydratase (EC 4.2.1.49) (characterized)
to candidate 352221 BT2694 putative urocanate hydratase (NCBI ptt file)

Query= reanno::SB2B:6937476
         (670 letters)



>FitnessBrowser__Btheta:352221
          Length = 663

 Score =  616 bits (1588), Expect = e-180
 Identities = 315/624 (50%), Positives = 408/624 (65%), Gaps = 16/624 (2%)

Query: 24  PYPA---DANRAPKRKDILTAAEKQLAVRNALRYFPAEWHQELAAEFAKELNDFGRIYMY 80
           PYPA      RAP R  +LT A+   A++NALRY P E H++LA EF +EL   GRIY Y
Sbjct: 11  PYPAFIEGIRRAPDRSYMLTPAQTATALKNALRYIPLELHEQLAPEFMEELRTRGRIYGY 70

Query: 81  RFKPEYAMKARAISEYPAKCEQAAAIMLMVDNNLDPAVAQHPEELITYGGNGAVFQNWAQ 140
           RF+P   +KAR I EY  KC +  A  +M+DNNL   +A +P EL+TYG  G V QNW Q
Sbjct: 71  RFRPAGDLKARPIDEYRGKCVEGKAFQVMIDNNLCFDIALYPYELVTYGETGQVCQNWMQ 130

Query: 141 YRLTMKYLSEMEADQTLHLYSGHPMGLFPSSVDAPRVVVTNGMMIPNYSKPDDWERFNAL 200
           Y L  +YL E+  +QTL + SGHP+GLF S  DAPRV++TN MMI  +    DW     +
Sbjct: 131 YLLIKQYLEELTPEQTLVIESGHPLGLFRSRPDAPRVIITNSMMIGQFDNQHDWHIAAQM 190

Query: 201 GVTQYGQMTAGSFMYIGPQGIVHGTTITVMNGFRKVL--EKGDSPKGKIFLTAGLGGMSG 258
           GV  YGQMTAG +MYIGPQGIVHGT  T++N  R  L   +    +G +F+++GLGGMSG
Sbjct: 191 GVANYGQMTAGGWMYIGPQGIVHGTFNTLLNAGRLKLGIPQDKDLRGHLFVSSGLGGMSG 250

Query: 259 AQPKAGNIAGCITVCAEVNPKAATKRHAQGWVDELIDNMDALVARVKQAQANEEVVSIAF 318
           AQPKA  IAG  ++ AEV+      R+ QGWV  +  ++       K+A    E  SIA+
Sbjct: 251 AQPKAAEIAGAASIIAEVDSSRIETRYRQGWVGHVTQDLSEAFRLAKEAMERREPCSIAY 310

Query: 319 IGNVVNVWEAFDEHDIFVHLGSDQTSLHNPWSGGYYPVDISYDESNRLIREEPELFKTKV 378
            GNVV++ E  +   I + L SDQTS H  + GGY PV ++++E  RL+ E P+ F+   
Sbjct: 311 HGNVVDLLEYAEREQIHIELLSDQTSCHAVYEGGYCPVGLTFEERTRLLHESPDQFRRLA 370

Query: 379 QATLKRHADAINRHTAKGTYFFDYGNAFLLEASRAGGDVMAENGID----FKYPSYVQDI 434
            A+L+RH + I +  A GTYFFDYGN+F+     AG   ++ NG+D    F +PSYV+DI
Sbjct: 371 DASLRRHFEVIRKLVACGTYFFDYGNSFMKAIYDAGVKEISRNGVDEKDGFIWPSYVEDI 430

Query: 435 LGPMCFDYGFGPFRWVCTSGNSADLDRTDAIAAEVLARIMAEAPAEIQQQMQDNITWIKD 494
           +GP  FDYG+GPFRWVC SG   DL +TD  A E +           + Q  DN  WI+D
Sbjct: 431 MGPQLFDYGYGPFRWVCLSGRHEDLIKTDRAAMECI-------DVNRRGQDLDNYNWIRD 483

Query: 495 AKQNKLVVGSQARILYADAEGRMEIAKAFNDAISRGEIGPVVLGRDHHDVSGTDSPFRET 554
           A++N+LVVG+QARILY DA GRM IA  FN+ + RGE+GP++LGRDHHDVSGTDSPFRET
Sbjct: 484 AEKNRLVVGTQARILYQDAVGRMNIALRFNEMVRRGEVGPIMLGRDHHDVSGTDSPFRET 543

Query: 555 SNIYDGSRFTADMAIHNVIGDSFRGATWVSIHNGGGVGWGEVINGGFGMLLDGTEAAERR 614
           SNI DGS   ADMA+    G+  RG + V++HNGGGVG G+ INGGFGM+ DG+E  +  
Sbjct: 544 SNIKDGSNVMADMAVQCFAGNCARGMSLVALHNGGGVGIGKAINGGFGMVCDGSERVDEI 603

Query: 615 LKSMLLFDVNNGIARRSWARNEEA 638
           L+S +L+DV  G+ARRSWARN  A
Sbjct: 604 LRSAMLWDVMGGVARRSWARNPHA 627


Lambda     K      H
   0.318    0.134    0.404 

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: 1141
Number of extensions: 40
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 670
Length of database: 663
Length adjustment: 38
Effective length of query: 632
Effective length of database: 625
Effective search space:   395000
Effective search space used:   395000
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: 54 (25.4 bits)

Align candidate 352221 BT2694 (putative urocanate hydratase (NCBI ptt file))
to HMM TIGR01228 (hutU: urocanate hydratase (EC 4.2.1.49))

# 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.carbon/TIGR01228.hmm
# target sequence database:        /tmp/gapView.29227.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01228  [M=545]
Accession:   TIGR01228
Description: hutU: urocanate hydratase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   1.1e-131  426.0   0.1   1.4e-131  425.7   0.1    1.0  1  lcl|FitnessBrowser__Btheta:352221  BT2694 putative urocanate hydrat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:352221  BT2694 putative urocanate hydratase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  425.7   0.1  1.4e-131  1.4e-131      13     537 ..      88     632 ..      77     638 .. 0.94

  Alignments for each domain:
  == domain 1  score: 425.7 bits;  conditional E-value: 1.4e-131
                          TIGR01228  13 akgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafdkiveelkrleddetllvqsGkpvgvfkthek 88 
                                         k  e +a + ++ nnl  ++a  p elv yG +G+  +nw  +  i + l+ l  ++tl+++sG p+g+f+++ +
  lcl|FitnessBrowser__Btheta:352221  88 GKCVEGKAFQVMIDNNLCFDIALYPYELVTYGETGQVCQNWMQYLLIKQYLEELTPEQTLVIESGHPLGLFRSRPD 163
                                        55666778899***************************************************************** PP

                          TIGR01228  89 aprvliansnlvpkwadwekfeeleakGlimyGqmtaGswiyiGtqGilqGtyetlaelarkhfgg....slkgkl 160
                                        aprv+i+ns +++++ +++ ++   + G++ yGqmtaG w+yiG qGi+ Gt++tl +++r + g     +l+g+l
  lcl|FitnessBrowser__Btheta:352221 164 APRVIITNSMMIGQFDNQHDWHIAAQMGVANYGQMTAGGWMYIGPQGIVHGTFNTLLNAGRLKLGIpqdkDLRGHL 239
                                        **************************************************************998444569***** PP

                          TIGR01228 161 vltaGlGgmGGaqplavtlneavsiavevdeeridkrletkyldektddldealaraeeakaeGkalsigllGnaa 236
                                         +++GlGgm Gaqp a+++++a+si +evd +ri+ r ++ ++ ++t+dl ea++ a+ea+++ ++ si+ +Gn  
  lcl|FitnessBrowser__Btheta:352221 240 FVSSGLGGMSGAQPKAAEIAGAASIIAEVDSSRIETRYRQGWVGHVTQDLSEAFRLAKEAMERREPCSIAYHGNVV 315
                                        **************************************************************************** PP

                          TIGR01228 237 evleellergvvpdvvtdqtsahdell.GyipegytvedadklrdeepeeyvkaakaslakhvrallalqkkGavt 311
                                        ++le   + ++++++++dqts h     Gy p g t e+ ++l +e+p+++++ a asl +h + + +l   G+  
  lcl|FitnessBrowser__Btheta:352221 316 DLLEYAEREQIHIELLSDQTSCHAVYEgGYCPVGLTFEERTRLLHESPDQFRRLADASLRRHFEVIRKLVACGTYF 391
                                        ***********************987637*********************************************** PP

                          TIGR01228 312 fdyGnnirqvakeeG..........vedafdfpGfvpayird.lfceGkGpfrwvalsGdpadiyrtdkavkelfp 376
                                        fdyGn + +   ++G           +d f +p +v   + + lf  G Gpfrwv lsG  +d+ +td+a +e ++
  lcl|FitnessBrowser__Btheta:352221 392 FDYGNSFMKAIYDAGvkeisrngvdEKDGFIWPSYVEDIMGPqLFDYGYGPFRWVCLSGRHEDLIKTDRAAMECID 467
                                        ***************9999999988899999999999988754899**************************9997 PP

                          TIGR01228 377 ed...eel..hrwidlakekvafqGlparicwlgygereklalainelvrsGelkapvvigrdhldaGsvaspnre 447
                                         +   ++l   +wi  a+++    G  ari +     r ++al++ne+vr Ge+  p+++grdh+d     sp+re
  lcl|FitnessBrowser__Btheta:352221 468 VNrrgQDLdnYNWIRDAEKNRLVVGTQARILYQDAVGRMNIALRFNEMVRRGEV-GPIMLGRDHHDVSGTDSPFRE 542
                                        651113442258*****999999******************************9.6******************** PP

                          TIGR01228 448 teamkdGsdavadwpllnallntaaGaswvslhhGGGvglGfslhaglvivadGtdeaaerlkrvltadpGlGvir 523
                                        t ++kdGs+ +ad ++  +  n a G s+v+lh+GGGvg+G ++  g+ +v+dG++  +e l+ ++  d   Gv r
  lcl|FitnessBrowser__Btheta:352221 543 TSNIKDGSNVMADMAVQCFAGNCARGMSLVALHNGGGVGIGKAINGGFGMVCDGSERVDEILRSAMLWDVMGGVAR 618
                                        **********************************************************************99**** PP

                          TIGR01228 524 hadaGyesaldvak 537
                                         + a   +a+++ +
  lcl|FitnessBrowser__Btheta:352221 619 RSWARNPHAMETSD 632
                                        99998888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (545 nodes)
Target sequences:                          1  (663 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: 00:00:00.04
# Mc/sec: 8.22
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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

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 catabolism of small carbon sources