GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Shewanella sp. ANA-3

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate 7023380 Shewana3_0610 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)

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



>FitnessBrowser__ANA3:7023380
          Length = 405

 Score =  541 bits (1394), Expect = e-158
 Identities = 266/406 (65%), Positives = 326/406 (80%), Gaps = 1/406 (0%)

Query: 1   MSVEHAAVERADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAH 60
           MSV+   + RA FD VMVPNYAPAA IPVRG GSRVWDQ G E IDFAGGIAVN LGH H
Sbjct: 1   MSVD-MKLNRAQFDAVMVPNYAPAAVIPVRGEGSRVWDQEGNEFIDFAGGIAVNCLGHCH 59

Query: 61  PALVAALTEQANKLWHVSNVFTNEPALRLAHKLVDATFAERVFFCNSGAEANEAAFKLAR 120
           PALV AL  Q  KLWH+SNV TNEPAL LA KLV++TFAERV+F NSGAEANEAA KLAR
Sbjct: 60  PALVNALKTQGEKLWHLSNVMTNEPALELATKLVNSTFAERVYFANSGAEANEAALKLAR 119

Query: 121 RVAHDRFGTEKYEIVAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALK 180
           R A ++FG EK EI+A   +FHGRT FTV+VGGQ+ YSDGFGPK   ITH+PYND+AAL+
Sbjct: 120 RYALEKFGVEKDEIIAFDKAFHGRTFFTVSVGGQAAYSDGFGPKPQSITHLPYNDVAALE 179

Query: 181 AAVSDKTCAVVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFA 240
           AAVSDKTCA++LEP+QGEGG++ A+ ++L+  REL + HNAL++FDEVQTG+GR+G+L+A
Sbjct: 180 AAVSDKTCAIMLEPLQGEGGIIDADPAFLKAVRELANKHNALVIFDEVQTGVGRTGELYA 239

Query: 241 YQHYGVTPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVID 300
           Y    + PDILT+AK+LGGGFPIAAMLTT ++A+HL VGTHG+TYGGNPLACA+  AV+D
Sbjct: 240 YMGTDIVPDILTTAKALGGGFPIAAMLTTAEIAEHLKVGTHGSTYGGNPLACAIGNAVLD 299

Query: 301 VINTPEVLNGVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGKAKDIFNA 360
           V+NTPEVLNGV  +    +  L +I EKY +F+E+RG GLLLG VL++ ++G+++D   A
Sbjct: 300 VVNTPEVLNGVKHREQLLRDGLNKINEKYHVFSEIRGKGLLLGAVLNEQYQGRSRDFLVA 359

Query: 361 AEREGLMILQAGPDVIRFAPSLVVEDADIDAGLDRFERAAAKLTQA 406
           +  EGLM L AG +V+RFAPSLV+ +ADI  GL RFERA A +  A
Sbjct: 360 SVAEGLMSLMAGANVVRFAPSLVIPEADIAEGLARFERAVASIAAA 405


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: 509
Number of extensions: 11
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: 405
Length adjustment: 31
Effective length of query: 375
Effective length of database: 374
Effective search space:   140250
Effective search space used:   140250
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 7023380 Shewana3_0610 (bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq))
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.aa/TIGR03246.hmm
# target sequence database:        /tmp/gapView.2083.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
     9e-213  692.4   1.1     1e-212  692.2   1.1    1.0  1  lcl|FitnessBrowser__ANA3:7023380  Shewana3_0610 bifunctional N-suc


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7023380  Shewana3_0610 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithi
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  692.2   1.1    1e-212    1e-212       2     396 ..       8     402 ..       7     403 .. 0.99

  Alignments for each domain:
  == domain 1  score: 692.2 bits;  conditional E-value: 1e-212
                         TIGR03246   2 eresfdevmvpvyapakfipvrgeGsrvwdqegkeyidfaGGiavnalGhahpelvealkeqaeklwhlgngytnep 78 
                                       +r++fd vmvp+yapa++ipvrgeGsrvwdqeg+e+idfaGGiavn+lGh+hp+lv+alk q+eklwhl+n++tnep
  lcl|FitnessBrowser__ANA3:7023380   8 NRAQFDAVMVPNYAPAAVIPVRGEGSRVWDQEGNEFIDFAGGIAVNCLGHCHPALVNALKTQGEKLWHLSNVMTNEP 84 
                                       89*************************************************************************** PP

                         TIGR03246  79 vlrlakklvdatfadkvffcnsGaeaneaalklarkvaldkygaekseivafknsfhGrtlftvsvGGqakysedfa 155
                                       +l+la klv++tfa++v+f+nsGaeaneaalklar++al+k+g ek+ei+af ++fhGrt+ftvsvGGqa+ys++f+
  lcl|FitnessBrowser__ANA3:7023380  85 ALELATKLVNSTFAERVYFANSGAEANEAALKLARRYALEKFGVEKDEIIAFDKAFHGRTFFTVSVGGQAAYSDGFG 161
                                       ***************************************************************************** PP

                         TIGR03246 156 plpegikhaayndlealkalisdktcavivepiqGegGvvpadkaflkglrelcdrhnallifdevqtGvGrtGely 232
                                       p+p+ i+h++ynd++al+a++sdktca+++ep+qGegG++ ad+aflk++rel ++hnal+ifdevqtGvGrtGely
  lcl|FitnessBrowser__ANA3:7023380 162 PKPQSITHLPYNDVAALEAAVSDKTCAIMLEPLQGEGGIIDADPAFLKAVRELANKHNALVIFDEVQTGVGRTGELY 238
                                       ***************************************************************************** PP

                         TIGR03246 233 aymeyGvtpdiltsakalGgGfpiGalltteelakvlkvGthGttyGGnplacavaekvldlvntaelleGvkqrhe 309
                                       aym + ++pdilt+akalGgGfpi a+ltt e+a++lkvGthG+tyGGnplaca+ ++vld+vnt+e+l+Gvk+r++
  lcl|FitnessBrowser__ANA3:7023380 239 AYMGTDIVPDILTTAKALGGGFPIAAMLTTAEIAEHLKVGTHGSTYGGNPLACAIGNAVLDVVNTPEVLNGVKHREQ 315
                                       ***************************************************************************** PP

                         TIGR03246 310 lfvdelekinarykvfseirGkGlliGavlteeyaGkakdlvnaaaeeGvlvliaGpdvvrfapslvieeeeikeGl 386
                                       l+ d l+kin++y+vfseirGkGll+Gavl+e+y+G+++d++ a+ +eG++ l+aG++vvrfapslvi+e++i+eGl
  lcl|FitnessBrowser__ANA3:7023380 316 LLRDGLNKINEKYHVFSEIRGKGLLLGAVLNEQYQGRSRDFLVASVAEGLMSLMAGANVVRFAPSLVIPEADIAEGL 392
                                       ***************************************************************************** PP

                         TIGR03246 387 arlekavekl 396
                                       ar+e+av+++
  lcl|FitnessBrowser__ANA3:7023380 393 ARFERAVASI 402
                                       *******976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (397 nodes)
Target sequences:                          1  (405 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 8.54
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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