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

GapMind for catabolism of small carbon sources

Aligments 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.3001.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: 00:00:00.02
# Mc/sec: 7.63
//
[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, or view the source code.

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