Alignments for a candidate for argD'B in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for argD'B in Shewanella oneidensis MR-1

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate 199805 SO0617 acetylornithine aminotransferase (NCBI ptt file)

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



>FitnessBrowser__MR1:199805
          Length = 405

 Score =  537 bits (1384), Expect = e-157
 Identities = 265/406 (65%), Positives = 325/406 (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 ++ G EK EI+A   +FHGRT FTV+VGGQ+ YSDGFGPK   ITH+P+ND+AAL+
Sbjct: 120 RYALEKHGVEKDEIIAFDKAFHGRTFFTVSVGGQAAYSDGFGPKPQSITHLPFNDVAALE 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 YMGTDIVPDILTTAKALGGGFPIAAMLTTTEIAEHLKVGTHGSTYGGNPLACAIGNAVLD 299

Query: 301 VINTPEVLNGVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGKAKDIFNA 360
           V+NTPEVLNGV  +    +  L +I EKY +F+EVRG GLLLG VL++ ++G+++D   A
Sbjct: 300 VVNTPEVLNGVKHREQLLRDGLNKINEKYHVFSEVRGKGLLLGAVLNEQYQGRSRDFLVA 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: 513
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 199805 SO0617 (acetylornithine aminotransferase (NCBI ptt file))
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.15700.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   5.2e-213  693.2   1.2   5.9e-213  693.0   1.2    1.0  1  lcl|FitnessBrowser__MR1:199805  SO0617 acetylornithine aminotran


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:199805  SO0617 acetylornithine aminotransferase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  693.0   1.2  5.9e-213  5.9e-213       2     396 ..       8     402 ..       7     403 .. 0.99

  Alignments for each domain:
  == domain 1  score: 693.0 bits;  conditional E-value: 5.9e-213
                       TIGR03246   2 eresfdevmvpvyapakfipvrgeGsrvwdqegkeyidfaGGiavnalGhahpelvealkeqaeklwhlgngytnepvl 80 
                                     +r++fd vmvp+yapa++ipvrgeGsrvwdqeg+e+idfaGGiavn+lGh+hp+lv+alk q+eklwhl+n++tnep+l
  lcl|FitnessBrowser__MR1:199805   8 NRAQFDAVMVPNYAPAAVIPVRGEGSRVWDQEGNEFIDFAGGIAVNCLGHCHPALVNALKTQGEKLWHLSNVMTNEPAL 86 
                                     89***************************************************************************** PP

                       TIGR03246  81 rlakklvdatfadkvffcnsGaeaneaalklarkvaldkygaekseivafknsfhGrtlftvsvGGqakysedfaplpe 159
                                     +la klv++tfa++v+f+nsGaeaneaalklar++al+k+g ek+ei+af ++fhGrt+ftvsvGGqa+ys++f+p+p+
  lcl|FitnessBrowser__MR1:199805  87 ELATKLVNSTFAERVYFANSGAEANEAALKLARRYALEKHGVEKDEIIAFDKAFHGRTFFTVSVGGQAAYSDGFGPKPQ 165
                                     ******************************************************************************* PP

                       TIGR03246 160 gikhaayndlealkalisdktcavivepiqGegGvvpadkaflkglrelcdrhnallifdevqtGvGrtGelyaymeyG 238
                                      i+h+++nd++al+a++sdktca+++ep+qGegG++ ad+aflk++rel ++hnal+ifdevqtGvGrtGelyaym + 
  lcl|FitnessBrowser__MR1:199805 166 SITHLPFNDVAALEAAVSDKTCAIMLEPLQGEGGIIDADPAFLKAVRELANKHNALVIFDEVQTGVGRTGELYAYMGTD 244
                                     ******************************************************************************* PP

                       TIGR03246 239 vtpdiltsakalGgGfpiGalltteelakvlkvGthGttyGGnplacavaekvldlvntaelleGvkqrhelfvdelek 317
                                     ++pdilt+akalGgGfpi a+ltt+e+a++lkvGthG+tyGGnplaca+ ++vld+vnt+e+l+Gvk+r++l+ d l+k
  lcl|FitnessBrowser__MR1:199805 245 IVPDILTTAKALGGGFPIAAMLTTTEIAEHLKVGTHGSTYGGNPLACAIGNAVLDVVNTPEVLNGVKHREQLLRDGLNK 323
                                     ******************************************************************************* PP

                       TIGR03246 318 inarykvfseirGkGlliGavlteeyaGkakdlvnaaaeeGvlvliaGpdvvrfapslvieeeeikeGlarlekavekl 396
                                     in++y+vfse+rGkGll+Gavl+e+y+G+++d++ a+ +eG++ l+aG++vvrfapslvi+e++i+eGlar+e+av+++
  lcl|FitnessBrowser__MR1:199805 324 INEKYHVFSEVRGKGLLLGAVLNEQYQGRSRDFLVASVAEGLMSLMAGANVVRFAPSLVIPEADIAEGLARFERAVASI 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.91
//
[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:

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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis