GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PAH in Dyella japonica UNC79MFTsu3.2

Align phenylalanine 4-monooxygenase (EC 1.14.16.1) (characterized)
to candidate N515DRAFT_3052 N515DRAFT_3052 Phenylalanine 4-hydroxylase

Query= BRENDA::P30967
         (297 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3052
          Length = 297

 Score =  367 bits (943), Expect = e-106
 Identities = 174/268 (64%), Positives = 207/268 (77%), Gaps = 2/268 (0%)

Query: 31  QPLDRYSAEDHATWATLYQRQCKLLPGRACDEFMEGLERLEVDADRVPDFNKLNQKLMAA 90
           QP   YS  DH  W TLY+RQ +LL GRAC EF++G+ER  +  + +P F  LN+ L   
Sbjct: 29  QPWADYSQTDHEVWNTLYRRQRELLKGRACQEFLDGIERFGMGENGIPKFADLNKVLGET 88

Query: 91  TGWKIVAVPGLIPDDVFFEHLANRRFPVTWWLREPHQLDYLQEPDVFHDLFGHVPLLINP 150
           TGW++VAV GL+PD+VFF+HLANRRFPV+WW+R P QLDYL EPD+FHDLFGHVPLL+NP
Sbjct: 89  TGWELVAVEGLLPDEVFFDHLANRRFPVSWWIRRPDQLDYLSEPDLFHDLFGHVPLLLNP 148

Query: 151 VFADYLEAYGKGGVKAKALG--ALPMLARLYWYTVEFGLINTPAGMRIYGAGILSSKSES 208
           VFADY++AYG+GG+KA  +G  AL  L RLYWYTVEFGLINT  GMRIYGAGI+SSK ES
Sbjct: 149 VFADYMQAYGRGGMKAFGIGPEALMNLTRLYWYTVEFGLINTSEGMRIYGAGIVSSKGES 208

Query: 209 IYCLDSASPNRVGFDLMRIMNTRYRIDTFQKTYFVIDSFKQLFDATAPDFAPLYLQLADA 268
           IYCLDSA+PNR+GF L R+MNTRYRIDTFQ+TYFVIDSF+QLFDAT PDF P+Y  L   
Sbjct: 209 IYCLDSAAPNRIGFGLERVMNTRYRIDTFQQTYFVIDSFEQLFDATRPDFTPIYADLKTR 268

Query: 269 QPWGAGDVAPDDLVLNAGDRQGWADTED 296
           +   A DV   D V   G R+G+A   D
Sbjct: 269 EAHAAADVLDSDRVFTRGTREGFATDAD 296


Lambda     K      H
   0.323    0.140    0.445 

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: 378
Number of extensions: 12
Number of successful extensions: 2
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: 297
Length of database: 297
Length adjustment: 26
Effective length of query: 271
Effective length of database: 271
Effective search space:    73441
Effective search space used:    73441
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 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate N515DRAFT_3052 N515DRAFT_3052 (Phenylalanine 4-hydroxylase)
to HMM TIGR01267 (phhA: phenylalanine-4-hydroxylase (EC 1.14.16.1))

# 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/TIGR01267.hmm
# target sequence database:        /tmp/gapView.32499.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01267  [M=248]
Accession:   TIGR01267
Description: Phe4hydrox_mono: phenylalanine-4-hydroxylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.2e-117  377.6   0.0   1.4e-117  377.3   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_3052  N515DRAFT_3052 Phenylalanine 4-h


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_3052  N515DRAFT_3052 Phenylalanine 4-hydroxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  377.3   0.0  1.4e-117  1.4e-117       4     248 .]      27     274 ..      24     274 .. 0.97

  Alignments for each domain:
  == domain 1  score: 377.3 bits;  conditional E-value: 1.4e-117
                                    TIGR01267   4 vaqdldryseeehavwatlidrqlkllegracdeyldGveklgldadripdleevneklraltGwk 69 
                                                  v+q++  ys+++h+vw+tl+ rq  ll+grac+e+ldG+e++g+  + ip++ ++n++l ++tGw+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3052  27 VEQPWADYSQTDHEVWNTLYRRQRELLKGRACQEFLDGIERFGMGENGIPKFADLNKVLGETTGWE 92 
                                                  689999************************************************************ PP

                                    TIGR01267  70 ivavpglipadvffehlanrrfpvttflrtpeeldylqepdvfhdlfGhvpllsnpvfadfleayG 135
                                                  +vav gl+p++vff+hlanrrfpv++++r p++ldyl epd+fhdlfGhvpll npvfad+++ayG
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3052  93 LVAVEGLLPDEVFFDHLANRRFPVSWWIRRPDQLDYLSEPDLFHDLFGHVPLLLNPVFADYMQAYG 158
                                                  ****************************************************************** PP

                                    TIGR01267 136 kkgvkakalgaa...llarlywytvefGlvetaaglriyGaGilsskkelvyaleskeplrvafdl 198
                                                  ++g+ka   g +    l+rlywytvefGl++t++g+riyGaGi+ssk e++y+l+s+ p+r++f l
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3052 159 RGGMKAFGIGPEalmNLTRLYWYTVEFGLINTSEGMRIYGAGIVSSKGESIYCLDSAAPNRIGFGL 224
                                                  ******98876544579************************************************* PP

                                    TIGR01267 199 levmrtryridklqkayfvlpslkrlfdaaqedfealvaeakdlkaldpa 248
                                                  ++vm+tryrid++q++yfv++s+++lfda+++df++++a++k  +a+++a
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3052 225 ERVMNTRYRIDTFQQTYFVIDSFEQLFDATRPDFTPIYADLKTREAHAAA 274
                                                  ********************************************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (248 nodes)
Target sequences:                          1  (297 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 6.93
//
[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