GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutI in Acidovorax sp. GW101-3H11

Align Imidazolonepropionase (EC 3.5.2.7) (characterized)
to candidate Ac3H11_2550 Imidazolonepropionase (EC 3.5.2.7)

Query= reanno::acidovorax_3H11:Ac3H11_2550
         (429 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2550
          Length = 429

 Score =  860 bits (2223), Expect = 0.0
 Identities = 429/429 (100%), Positives = 429/429 (100%)

Query: 1   VGRQMQHMDNHGHPSGSAASQNADGVWHNLQPAPGLWVADVAVPEGQPACVVVQQGQMAW 60
           VGRQMQHMDNHGHPSGSAASQNADGVWHNLQPAPGLWVADVAVPEGQPACVVVQQGQMAW
Sbjct: 1   VGRQMQHMDNHGHPSGSAASQNADGVWHNLQPAPGLWVADVAVPEGQPACVVVQQGQMAW 60

Query: 61  VGPEAQLPAAYKALSRHDARGALATPGLVDCHTHLVYGGQRANEFAMRLAGATYEEVAQA 120
           VGPEAQLPAAYKALSRHDARGALATPGLVDCHTHLVYGGQRANEFAMRLAGATYEEVAQA
Sbjct: 61  VGPEAQLPAAYKALSRHDARGALATPGLVDCHTHLVYGGQRANEFAMRLAGATYEEVAQA 120

Query: 121 GGGIVSSVKATRAASEDELFAQAAPRLQALLDEGVCAIEIKSGYGLALEHERKQLRVARR 180
           GGGIVSSVKATRAASEDELFAQAAPRLQALLDEGVCAIEIKSGYGLALEHERKQLRVARR
Sbjct: 121 GGGIVSSVKATRAASEDELFAQAAPRLQALLDEGVCAIEIKSGYGLALEHERKQLRVARR 180

Query: 181 LGEVFGVTVRTTFLGAHALPSEYAGRSGDYTDLVCNEMLPALAAEGLVDAVDVFCERIAF 240
           LGEVFGVTVRTTFLGAHALPSEYAGRSGDYTDLVCNEMLPALAAEGLVDAVDVFCERIAF
Sbjct: 181 LGEVFGVTVRTTFLGAHALPSEYAGRSGDYTDLVCNEMLPALAAEGLVDAVDVFCERIAF 240

Query: 241 TLAETEQVFQAAQKLGIPVKLHAEQLSDMGGSALAARYGALSCDHIEHLSADGIAAMKAA 300
           TLAETEQVFQAAQKLGIPVKLHAEQLSDMGGSALAARYGALSCDHIEHLSADGIAAMKAA
Sbjct: 241 TLAETEQVFQAAQKLGIPVKLHAEQLSDMGGSALAARYGALSCDHIEHLSADGIAAMKAA 300

Query: 301 GTVAVLLPGAYYTLRDTHLPPIAQLREAGVPMAVSTDHNPGTSPALSLLLMANMACTLFR 360
           GTVAVLLPGAYYTLRDTHLPPIAQLREAGVPMAVSTDHNPGTSPALSLLLMANMACTLFR
Sbjct: 301 GTVAVLLPGAYYTLRDTHLPPIAQLREAGVPMAVSTDHNPGTSPALSLLLMANMACTLFR 360

Query: 361 LTVPEALAGITTHAARALGLQDSHGLIASGRPANFVLWPVGEAAELAYWFGQKPACTIVR 420
           LTVPEALAGITTHAARALGLQDSHGLIASGRPANFVLWPVGEAAELAYWFGQKPACTIVR
Sbjct: 361 LTVPEALAGITTHAARALGLQDSHGLIASGRPANFVLWPVGEAAELAYWFGQKPACTIVR 420

Query: 421 QGCIHGVMP 429
           QGCIHGVMP
Sbjct: 421 QGCIHGVMP 429


Lambda     K      H
   0.319    0.133    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: 857
Number of extensions: 19
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: 429
Length of database: 429
Length adjustment: 32
Effective length of query: 397
Effective length of database: 397
Effective search space:   157609
Effective search space used:   157609
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 Ac3H11_2550 (Imidazolonepropionase (EC 3.5.2.7))
to HMM TIGR01224 (hutI: imidazolonepropionase (EC 3.5.2.7))

# 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/TIGR01224.hmm
# target sequence database:        /tmp/gapView.27555.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01224  [M=377]
Accession:   TIGR01224
Description: hutI: imidazolonepropionase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   9.1e-144  464.8   0.2   1.1e-143  464.6   0.2    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2550  Imidazolonepropionase (EC 3.5.2.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2550  Imidazolonepropionase (EC 3.5.2.7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  464.6   0.2  1.1e-143  1.1e-143       4     375 ..      49     422 ..      46     424 .. 0.98

  Alignments for each domain:
  == domain 1  score: 464.6 bits;  conditional E-value: 1.1e-143
                                        TIGR01224   4 aailveegkiaaigqkaalpge.eaakiidleGklvvPGlvDpHtHlvfagdRvkefelklq 64 
                                                      a ++v++g++a++g++a+lp+  +a+  +d+ G l++PGlvD+HtHlv++g+R++ef+++l+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2550  49 ACVVVQQGQMAWVGPEAQLPAAyKALSRHDARGALATPGLVDCHTHLVYGGQRANEFAMRLA 110
                                                      6899***************986599************************************* PP

                                        TIGR01224  65 GasYleilaeGgGilstvratraAseeellkeaeerlkkllrsGtttlEvKsGYGLdleaEl 126
                                                      Ga+Y+e++++GgGi+s v+atraAse+el+++a +rl+ ll +G+ ++E+KsGYGL le E 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2550 111 GATYEEVAQAGGGIVSSVKATRAASEDELFAQAAPRLQALLDEGVCAIEIKSGYGLALEHER 172
                                                      ************************************************************** PP

                                        TIGR01224 127 kmLrvikalkeelpvdvvttflgaHavPkevqededeyvdaileelipkvaeeklaeavDvF 188
                                                      k+Lrv+++l e + v v ttflgaHa+P e+ +++ +y+d +++e++p+ a e l++avDvF
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2550 173 KQLRVARRLGEVFGVTVRTTFLGAHALPSEYAGRSGDYTDLVCNEMLPALAAEGLVDAVDVF 234
                                                      ************************************************************** PP

                                        TIGR01224 189 cekgvFsveqsrrilkaaqeaGlavklHaeelkalggaelaaklgavsadHleeasdedika 250
                                                      ce+ +F+ ++++++++aaq+ G++vklHae+l+ +gg++laa+ ga+s dH+e++s+++i+a
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2550 235 CERIAFTLAETEQVFQAAQKLGIPVKLHAEQLSDMGGSALAARYGALSCDHIEHLSADGIAA 296
                                                      ************************************************************** PP

                                        TIGR01224 251 laeagtvavlLPgtaflLr.eaapparklidekvivalatDlnPgsspllslqlilslavtl 311
                                                      +++agtvavlLPg++++Lr ++ pp+ +l++++v++a++tD nPg+sp lsl l+ ++a+tl
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2550 297 MKAAGTVAVLLPGAYYTLRdTHLPPIAQLREAGVPMAVSTDHNPGTSPALSLLLMANMACTL 358
                                                      *******************9999*************************************** PP

                                        TIGR01224 312 lkltaeealaaatvnaAqalglgeekGtleeGkdadlvvlsaesyeeiaYrlgvnvveavik 373
                                                      ++lt +eala++t +aA algl++++G +++G+ a++v++ + + +e+aY++g +   +++ 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2550 359 FRLTVPEALAGITTHAARALGLQDSHGLIASGRPANFVLWPVGEAAELAYWFGQKPACTIVR 420
                                                      *****************************************************987777777 PP

                                        TIGR01224 374 nG 375
                                                      +G
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2550 421 QG 422
                                                      66 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (377 nodes)
Target sequences:                          1  (429 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: 11.92
//
[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:

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