Alignments for a candidate for hutF in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutF in Cupriavidus basilensis 4G11

Align Formiminoglutamic iminohydrolase (EC 3.5.3.13) (characterized)
to candidate RR42_RS16900 RR42_RS16900 N-formimino-L-glutamate deiminase

Query= reanno::acidovorax_3H11:Ac3H11_2549
         (464 letters)



>FitnessBrowser__Cup4G11:RR42_RS16900
          Length = 466

 Score =  552 bits (1423), Expect = e-162
 Identities = 284/460 (61%), Positives = 332/460 (72%), Gaps = 8/460 (1%)

Query: 9   LFAADALLPTGWARDVLVAWDGAGRITAVTPNAQPN-GAAVAPGPLLPGMPNLHSHAFQR 67
           LFA  ALLPTGWA DVL+AWD AG  T V   AQP      A GPLLPGMPNLHSHAFQR
Sbjct: 6   LFATQALLPTGWASDVLLAWDDAGAFTTVQAGAQPAVDVPRAAGPLLPGMPNLHSHAFQR 65

Query: 68  AFAGLTEYR------GESQDSFWSWRNLMYRFAARITPESLEAIATWLYVEMLEAGYTSV 121
            FAGLTE+R      G+  DSFWSWR LMYRFA R++P++LEAIAT LY+EML AGYTSV
Sbjct: 66  GFAGLTEFRSETLADGQQSDSFWSWRKLMYRFALRLSPDTLEAIATQLYIEMLRAGYTSV 125

Query: 122 CEFHYVHHDQDGRPYADDATLSLALLRAAKSAGIGITLLPVLYQTSGFGAKPPRADQARF 181
           CEFHYVHHD  G+PYAD A +SL LLRAA++AGIGITLLPVLYQT+GFG KP   DQ RF
Sbjct: 126 CEFHYVHHDTHGKPYADPAEMSLRLLRAAQTAGIGITLLPVLYQTAGFGDKPAVPDQRRF 185

Query: 182 IRSTDNMLSLLERLAPATRALGGILGLAPHSLRAVPPDSLAAAVQGLTALNPQAPIHIHI 241
           +  T  ML+LL RLAP        LGLAPHSLRAVPP SLA AV GL AL+  AP+HIHI
Sbjct: 186 LHETHAMLALLGRLAPQCHGQAR-LGLAPHSLRAVPPQSLADAVAGLHALDATAPVHIHI 244

Query: 242 AEQTQEVEDCIAWSGQRPVQWLLEHAPVDERWCLVHATHMTPQEYADAARTGAVAGICPT 301
           AEQ +EV++CI  +G RPV WLL+HA VD RWCLVHATH+   E    A +GAVAGICPT
Sbjct: 245 AEQQREVDECITLTGTRPVAWLLDHAEVDARWCLVHATHLDWDERRRLAHSGAVAGICPT 304

Query: 302 TEANLGDGIFDMPLWLQHGGRWGVGSDSHACVNAAEELLMLEYGQRLSLRQRNVLASRSQ 361
           TEANLGDG+FD   +L  GG WG+GSDSHA V+  EEL + EYGQRL+L++RNVLAS + 
Sbjct: 305 TEANLGDGVFDAAPYLGQGGVWGIGSDSHASVSVVEELRLFEYGQRLALQKRNVLASDAH 364

Query: 362 AEVATAMTLQAVQGGAQASGRSVSGLAVGQQADLVALDARHVALAGLPAPSMLSSHVFGS 421
            +VA  + L A  GGA+ASGR +  +AVGQQAD V LD  H AL+GL     L+ HVF +
Sbjct: 365 RQVADRLYLDAAFGGARASGRDIGAIAVGQQADFVVLDGAHPALSGLSGSQALAVHVFAN 424

Query: 422 HRTSAIDSLWVAGVLRVAQGRHALHDAAAQAFVAARSTTI 461
           H    +  +  AG +RV  G HAL   A + F AAR++ +
Sbjct: 425 HGHETLAEVRTAGRMRVQHGLHALQADAGKRFAAARASLL 464


Lambda     K      H
   0.320    0.132    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: 692
Number of extensions: 32
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: 464
Length of database: 466
Length adjustment: 33
Effective length of query: 431
Effective length of database: 433
Effective search space:   186623
Effective search space used:   186623
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: 51 (24.3 bits)

Align candidate RR42_RS16900 RR42_RS16900 (N-formimino-L-glutamate deiminase)
to HMM TIGR02022 (hutF: formiminoglutamate deiminase (EC 3.5.3.13))

# 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/TIGR02022.hmm
# target sequence database:        /tmp/gapView.7928.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02022  [M=455]
Accession:   TIGR02022
Description: hutF: formiminoglutamate deiminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.8e-179  582.5   8.3   3.2e-179  582.4   8.3    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS16900  RR42_RS16900 N-formimino-L-gluta


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS16900  RR42_RS16900 N-formimino-L-glutamate deiminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  582.4   8.3  3.2e-179  3.2e-179       4     453 ..       6     463 ..       3     465 .. 0.96

  Alignments for each domain:
  == domain 1  score: 582.4 bits;  conditional E-value: 3.2e-179
                                 TIGR02022   4 yfaerallpdgwaegvrlavaedGrilavetgvsaaedaerlsgvvlpglanlHsHAFqralaGlaeva 72 
                                               +fa +allp+gwa++v la +++G  ++v++g++ a d+ r +g++lpg++nlHsHAFqr++aGl+e +
  lcl|FitnessBrowser__Cup4G11:RR42_RS16900   6 LFATQALLPTGWASDVLLAWDDAGAFTTVQAGAQPAVDVPRAAGPLLPGMPNLHSHAFQRGFAGLTEFR 74 
                                               799***************************************************************988 PP

                                 TIGR02022  73 gsg......aDsFWtWRevmYrlverldPeqleaiarqlyvemlkaGftrvgEFHYlHHaadGtpYadp 135
                                               +++      +DsFW+WR +mYr++ rl+P++leaia qly+eml+aG+t+v EFHY+HH++ G+pYadp
  lcl|FitnessBrowser__Cup4G11:RR42_RS16900  75 SETladgqqSDSFWSWRKLMYRFALRLSPDTLEAIATQLYIEMLRAGYTSVCEFHYVHHDTHGKPYADP 143
                                               6655555559*********************************************************** PP

                                 TIGR02022 136 aelaeriaaAAadaGigltlLpvlYahagFGgaaanegqrrfiddveaflrlvealrkelaaqeearlG 204
                                               ae++ r+++AA++aGig+tlLpvlY  agFG ++a + qrrf++++ a l+l+ +l+++++   +arlG
  lcl|FitnessBrowser__Cup4G11:RR42_RS16900 144 AEMSLRLLRAAQTAGIGITLLPVLYQTAGFGDKPAVPDQRRFLHETHAMLALLGRLAPQCH--GQARLG 210
                                               ***********************************************************99..5799** PP

                                 TIGR02022 205 laiHslRAvtaeelaavlq...aserqlPvHiHvaEqqkEvddClaasgrrPvewLldhaevdarwclv 270
                                               la+HslRAv+++ la+ ++   a + ++PvHiH+aEqq+Evd+C+  +g rPv+wLldhaevdarwclv
  lcl|FitnessBrowser__Cup4G11:RR42_RS16900 211 LAPHSLRAVPPQSLADAVAglhALDATAPVHIHIAEQQREVDECITLTGTRPVAWLLDHAEVDARWCLV 279
                                               **************8765334488999****************************************** PP

                                 TIGR02022 271 HatHltdeevkllaksgavaglCpttEanLgDGifpaadfvaaggrlgiGsDshvvvdvleElRllEyg 339
                                               HatHl+ +e ++la+sgavag+CpttEanLgDG+f aa ++ +gg +giGsDsh++v+v+eElRl+Eyg
  lcl|FitnessBrowser__Cup4G11:RR42_RS16900 280 HATHLDWDERRRLAHSGAVAGICPTTEANLGDGVFDAAPYLGQGGVWGIGSDSHASVSVVEELRLFEYG 348
                                               ********************************************************************* PP

                                 TIGR02022 340 qRLrdraRnvlaageeasvaralydaAlaggaqalGlaegeleaGarADlltldledpslagakgdall 408
                                               qRL  ++Rnvla++ +++va++ly  A+ gga+a G++ g++++G++AD+++ld+++p+l g +g++ l
  lcl|FitnessBrowser__Cup4G11:RR42_RS16900 349 QRLALQKRNVLASDAHRQVADRLYLDAAFGGARASGRDIGAIAVGQQADFVVLDGAHPALSGLSGSQAL 417
                                               ********************************************************************* PP

                                 TIGR02022 409 dsllfaaek.aavrdvvvaGrkvvrdgrHaleeeierafakvlral 453
                                                  +fa ++ +++ +v  aGr  v++g Hal+++++++fa++  +l
  lcl|FitnessBrowser__Cup4G11:RR42_RS16900 418 AVHVFANHGhETLAEVRTAGRMRVQHGLHALQADAGKRFAAARASL 463
                                               ******86526799**************************987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (466 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: 00:00:00.02
# Mc/sec: 10.48
//
[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