GapMind for catabolism of small carbon sources

 

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

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate PfGW456L13_1971 Succinylornithine transaminase (EC 2.6.1.81)

Query= reanno::pseudo1_N1B4:Pf1N1B4_3440
         (406 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1971
          Length = 406

 Score =  775 bits (2001), Expect = 0.0
 Identities = 386/406 (95%), Positives = 397/406 (97%)

Query: 1   MSVEHAAVERADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAH 60
           MSVEHAAV+RADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAH
Sbjct: 1   MSVEHAAVQRADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAH 60

Query: 61  PALVAALTEQANKLWHVSNVFTNEPALRLAHKLVDATFAERVFFCNSGAEANEAAFKLAR 120
           PALV ALTEQANKLWHVSNVFTNEPALRLAHKLVDATFAER FFCNSGAEANEAAFKLAR
Sbjct: 61  PALVGALTEQANKLWHVSNVFTNEPALRLAHKLVDATFAERAFFCNSGAEANEAAFKLAR 120

Query: 121 RVAHDRFGTEKYEIVAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALK 180
           RVA DR+G+EKYEI+AALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALK
Sbjct: 121 RVAFDRYGSEKYEIIAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALK 180

Query: 181 AAVSDKTCAVVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFA 240
           AAVSDKTCAVVLEPIQGEGGVLPAEL+YLQGARELC+ HNALLVFDEVQTGMGR+G LFA
Sbjct: 181 AAVSDKTCAVVLEPIQGEGGVLPAELAYLQGARELCNEHNALLVFDEVQTGMGRTGHLFA 240

Query: 241 YQHYGVTPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVID 300
           YQHYGV PDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVA AVID
Sbjct: 241 YQHYGVIPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAGAVID 300

Query: 301 VINTPEVLNGVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGKAKDIFNA 360
           VINTPEVL GVNAKHDKFK RLEQIGEKYGLFT+VRGLGLL+GCVLSDAWKGKAKDIFNA
Sbjct: 301 VINTPEVLAGVNAKHDKFKARLEQIGEKYGLFTQVRGLGLLIGCVLSDAWKGKAKDIFNA 360

Query: 361 AEREGLMILQAGPDVIRFAPSLVVEDADIDAGLDRFERAAAKLTQA 406
           AE+EGLMILQAGPDV+RFAPSLVVEDADIDAGLDRFERAAAKLTQA
Sbjct: 361 AEQEGLMILQAGPDVVRFAPSLVVEDADIDAGLDRFERAAAKLTQA 406


Lambda     K      H
   0.320    0.136    0.400 

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: 657
Number of extensions: 7
Number of successful extensions: 1
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: 406
Length of database: 406
Length adjustment: 31
Effective length of query: 375
Effective length of database: 375
Effective search space:   140625
Effective search space used:   140625
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: 50 (23.9 bits)

Align candidate PfGW456L13_1971 (Succinylornithine transaminase (EC 2.6.1.81))
to HMM TIGR03246 (astC: succinylornithine transaminase family (EC 2.6.1.81))

# 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/TIGR03246.hmm
# target sequence database:        /tmp/gapView.31670.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03246  [M=397]
Accession:   TIGR03246
Description: arg_catab_astC: succinylornithine transaminase family
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   1.6e-220  717.9   1.6   1.9e-220  717.7   1.6    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1971  Succinylornithine transaminase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1971  Succinylornithine transaminase (EC 2.6.1.81)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  717.7   1.6  1.9e-220  1.9e-220       1     396 [.       8     403 ..       8     404 .. 1.00

  Alignments for each domain:
  == domain 1  score: 717.7 bits;  conditional E-value: 1.9e-220
                                               TIGR03246   1 veresfdevmvpvyapakfipvrgeGsrvwdqegkeyidfaGGiavnalGhahpe 55 
                                                             v+r++fd+vmvp+yapa+fipvrg Gsrvwdq+g+e+idfaGGiavn lGhahp+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1971   8 VQRADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPA 62 
                                                             79***************************************************** PP

                                               TIGR03246  56 lvealkeqaeklwhlgngytnepvlrlakklvdatfadkvffcnsGaeaneaalk 110
                                                             lv al+eqa+klwh++n++tnep+lrla+klvdatfa+++ffcnsGaeaneaa+k
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1971  63 LVGALTEQANKLWHVSNVFTNEPALRLAHKLVDATFAERAFFCNSGAEANEAAFK 117
                                                             ******************************************************* PP

                                               TIGR03246 111 larkvaldkygaekseivafknsfhGrtlftvsvGGqakysedfaplpegikhaa 165
                                                             lar+va+d+yg+ek+ei+a  nsfhGrtlftv vGGq+kys++f+p+++gi+h++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1971 118 LARRVAFDRYGSEKYEIIAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVP 172
                                                             ******************************************************* PP

                                               TIGR03246 166 yndlealkalisdktcavivepiqGegGvvpadkaflkglrelcdrhnallifde 220
                                                             yndl+alka++sdktcav++epiqGegGv+pa+ a+l+g+relc++hnall+fde
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1971 173 YNDLAALKAAVSDKTCAVVLEPIQGEGGVLPAELAYLQGARELCNEHNALLVFDE 227
                                                             ******************************************************* PP

                                               TIGR03246 221 vqtGvGrtGelyaymeyGvtpdiltsakalGgGfpiGalltteelakvlkvGthG 275
                                                             vqtG+GrtG+l+ay++yGv+pdiltsak+lGgGfpi a+ltte+lak+l vGthG
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1971 228 VQTGMGRTGHLFAYQHYGVIPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHG 282
                                                             ******************************************************* PP

                                               TIGR03246 276 ttyGGnplacavaekvldlvntaelleGvkqrhelfvdelekinarykvfseirG 330
                                                             ttyGGnplacava++v+d++nt+e+l+Gv+++h++f ++le+i+++y +f+++rG
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1971 283 TTYGGNPLACAVAGAVIDVINTPEVLAGVNAKHDKFKARLEQIGEKYGLFTQVRG 337
                                                             ******************************************************* PP

                                               TIGR03246 331 kGlliGavlteeyaGkakdlvnaaaeeGvlvliaGpdvvrfapslvieeeeikeG 385
                                                              GlliG+vl+++++Gkakd+ naa++eG+++l+aGpdvvrfapslv+e+++i+ G
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1971 338 LGLLIGCVLSDAWKGKAKDIFNAAEQEGLMILQAGPDVVRFAPSLVVEDADIDAG 392
                                                             ******************************************************* PP

                                               TIGR03246 386 larlekavekl 396
                                                             l+r+e+a +kl
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1971 393 LDRFERAAAKL 403
                                                             *******9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (397 nodes)
Target sequences:                          1  (406 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: 9.24
//
[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