Alignments for a candidate for astC in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for astC in Pseudomonas fluorescens FW300-N2E2

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate Pf6N2E2_5665 Succinylornithine transaminase (EC 2.6.1.81)

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



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5665
          Length = 406

 Score =  758 bits (1956), Expect = 0.0
 Identities = 377/406 (92%), Positives = 390/406 (96%)

Query: 1   MSVEHAAVERADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAH 60
           MSVE AAV+RADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAH
Sbjct: 1   MSVEQAAVQRADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAH 60

Query: 61  PALVAALTEQANKLWHVSNVFTNEPALRLAHKLVDATFAERVFFCNSGAEANEAAFKLAR 120
           PALV ALTEQANKLWHVSNVFTNEPALRLAHKLV+ATFAER FFCNSGAEANEAAFKLAR
Sbjct: 61  PALVGALTEQANKLWHVSNVFTNEPALRLAHKLVNATFAERAFFCNSGAEANEAAFKLAR 120

Query: 121 RVAHDRFGTEKYEIVAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALK 180
           RVA DRFG+EKYEI+AALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALK
Sbjct: 121 RVAFDRFGSEKYEIIAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALK 180

Query: 181 AAVSDKTCAVVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFA 240
           AA+SDKTCAVVLEPIQGEGGVLPAE +YLQGAR+LCDAH+ALLVFDEVQTGMGRSG LFA
Sbjct: 181 AAISDKTCAVVLEPIQGEGGVLPAEQAYLQGARDLCDAHDALLVFDEVQTGMGRSGHLFA 240

Query: 241 YQHYGVTPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVID 300
           Y HYGV PDILTSAKSLGGGFPIAAMLTTE LAKHLVVGTHGTTYGGNPLACAVAEAVID
Sbjct: 241 YMHYGVVPDILTSAKSLGGGFPIAAMLTTEALAKHLVVGTHGTTYGGNPLACAVAEAVID 300

Query: 301 VINTPEVLNGVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGKAKDIFNA 360
           V+NTPEVL GV  KH KFK RLEQIGEKYGLFT+VRGLGLL+GCVL+DAWKGKAKDIFNA
Sbjct: 301 VVNTPEVLGGVKTKHAKFKARLEQIGEKYGLFTQVRGLGLLIGCVLNDAWKGKAKDIFNA 360

Query: 361 AEREGLMILQAGPDVIRFAPSLVVEDADIDAGLDRFERAAAKLTQA 406
           AE+EGLMILQAGPDVIRFAPSLVVEDADID GLDRFERA AKLTQA
Sbjct: 361 AEQEGLMILQAGPDVIRFAPSLVVEDADIDEGLDRFERAVAKLTQA 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: 658
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 Pf6N2E2_5665 (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.31506.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
     1e-221  721.8   1.6   1.2e-221  721.7   1.6    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5665  Succinylornithine transaminase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5665  Succinylornithine transaminase (EC 2.6.1.81)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  721.7   1.6  1.2e-221  1.2e-221       1     396 [.       8     403 ..       8     404 .. 1.00

  Alignments for each domain:
  == domain 1  score: 721.7 bits;  conditional E-value: 1.2e-221
                                      TIGR03246   1 veresfdevmvpvyapakfipvrgeGsrvwdqegkeyidfaGGiavnalGhahpelvealkeqa 64 
                                                    v+r++fd+vmvp+yapa+fipvrg Gsrvwdq+g+e+idfaGGiavn lGhahp+lv al+eqa
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5665   8 VQRADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVGALTEQA 71 
                                                    79************************************************************** PP

                                      TIGR03246  65 eklwhlgngytnepvlrlakklvdatfadkvffcnsGaeaneaalklarkvaldkygaekseiv 128
                                                    +klwh++n++tnep+lrla+klv+atfa+++ffcnsGaeaneaa+klar+va+d++g+ek+ei+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5665  72 NKLWHVSNVFTNEPALRLAHKLVNATFAERAFFCNSGAEANEAAFKLARRVAFDRFGSEKYEII 135
                                                    **************************************************************** PP

                                      TIGR03246 129 afknsfhGrtlftvsvGGqakysedfaplpegikhaayndlealkalisdktcavivepiqGeg 192
                                                    a  nsfhGrtlftv vGGq+kys++f+p+++gi+h++yndl+alka+isdktcav++epiqGeg
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5665 136 AALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALKAAISDKTCAVVLEPIQGEG 199
                                                    **************************************************************** PP

                                      TIGR03246 193 GvvpadkaflkglrelcdrhnallifdevqtGvGrtGelyaymeyGvtpdiltsakalGgGfpi 256
                                                    Gv+pa++a+l+g+r+lcd+h+all+fdevqtG+Gr G+l+aym+yGv+pdiltsak+lGgGfpi
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5665 200 GVLPAEQAYLQGARDLCDAHDALLVFDEVQTGMGRSGHLFAYMHYGVVPDILTSAKSLGGGFPI 263
                                                    **************************************************************** PP

                                      TIGR03246 257 GalltteelakvlkvGthGttyGGnplacavaekvldlvntaelleGvkqrhelfvdelekina 320
                                                     a+ltte+lak+l vGthGttyGGnplacavae+v+d+vnt+e+l Gvk++h++f ++le+i++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5665 264 AAMLTTEALAKHLVVGTHGTTYGGNPLACAVAEAVIDVVNTPEVLGGVKTKHAKFKARLEQIGE 327
                                                    **************************************************************** PP

                                      TIGR03246 321 rykvfseirGkGlliGavlteeyaGkakdlvnaaaeeGvlvliaGpdvvrfapslvieeeeike 384
                                                    +y +f+++rG GlliG+vl+++++Gkakd+ naa++eG+++l+aGpdv+rfapslv+e+++i+e
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5665 328 KYGLFTQVRGLGLLIGCVLNDAWKGKAKDIFNAAEQEGLMILQAGPDVIRFAPSLVVEDADIDE 391
                                                    **************************************************************** PP

                                      TIGR03246 385 Glarlekavekl 396
                                                    Gl+r+e+av+kl
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5665 392 GLDRFERAVAKL 403
                                                    *********987 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.72
//
[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