Alignments for a candidate for astC in Stutzerimonas stutzeri A1501

GapMind for catabolism of small carbon sources

Alignments for a candidate for astC in Stutzerimonas stutzeri A1501

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_011912810.1 PST_RS08350 aspartate aminotransferase family protein

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



>NCBI__GCF_000013785.1:WP_011912810.1
          Length = 406

 Score =  669 bits (1727), Expect = 0.0
 Identities = 316/406 (77%), Positives = 364/406 (89%)

Query: 1   MSVEHAAVERADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAH 60
           MS  H  VERADFDQV+VP +APAAF+PVRG GSRVWDQSGREL+DFAGGIAVN LGHAH
Sbjct: 1   MSAPHTPVERADFDQVIVPTFAPAAFVPVRGLGSRVWDQSGRELVDFAGGIAVNALGHAH 60

Query: 61  PALVAALTEQANKLWHVSNVFTNEPALRLAHKLVDATFAERVFFCNSGAEANEAAFKLAR 120
           PA++AALTEQA KLWH+SN++TNEPALRLA KLV ATFA+R FFCNSGAEANE+AFKLAR
Sbjct: 61  PAMIAALTEQAGKLWHISNIYTNEPALRLAKKLVAATFADRAFFCNSGAEANESAFKLAR 120

Query: 121 RVAHDRFGTEKYEIVAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALK 180
           R AHD +G +K+EI++ALNSFHGRTLFTV VGGQSKYSDGFGPKI GITHVPYNDL ALK
Sbjct: 121 RYAHDVYGPQKFEIISALNSFHGRTLFTVTVGGQSKYSDGFGPKIEGITHVPYNDLEALK 180

Query: 181 AAVSDKTCAVVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFA 240
           AA+SDKTCAVVLEPIQGE G+LP E +YL+GAR+LC+ HNALL+FDEVQTG+GR+G+LFA
Sbjct: 181 AAISDKTCAVVLEPIQGESGILPGEQAYLEGARQLCNEHNALLIFDEVQTGLGRTGELFA 240

Query: 241 YQHYGVTPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVID 300
           Y HYGVTPDILT+AKSLGGGFPI AMLTT ++A H  VGTHGTTYGGNPLACAVAE V+D
Sbjct: 241 YMHYGVTPDILTNAKSLGGGFPIGAMLTTNEIAAHFSVGTHGTTYGGNPLACAVAETVLD 300

Query: 301 VINTPEVLNGVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGKAKDIFNA 360
           ++NTPEVL GV A+H++FK RL QIGE+YG+F++VRG GLL+GCVLSDAWKGKA   + A
Sbjct: 301 IVNTPEVLEGVKARHERFKARLLQIGERYGVFSQVRGRGLLIGCVLSDAWKGKAGAFWAA 360

Query: 361 AEREGLMILQAGPDVIRFAPSLVVEDADIDAGLDRFERAAAKLTQA 406
           AE+E LM+LQAGPDV+R APSL++++ADID GLDRFERA A LTQA
Sbjct: 361 AEKEALMVLQAGPDVVRLAPSLIIDEADIDEGLDRFERAIATLTQA 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: 584
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 WP_011912810.1 PST_RS08350 (aspartate aminotransferase family protein)
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.2879118.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.1e-218  708.9   0.2     1e-217  708.7   0.2    1.0  1  NCBI__GCF_000013785.1:WP_011912810.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000013785.1:WP_011912810.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  708.7   0.2    1e-217    1e-217       1     396 [.       8     403 ..       8     404 .. 1.00

  Alignments for each domain:
  == domain 1  score: 708.7 bits;  conditional E-value: 1e-217
                             TIGR03246   1 veresfdevmvpvyapakfipvrgeGsrvwdqegkeyidfaGGiavnalGhahpelvealkeqaeklwhlgng 73 
                                           ver++fd+v+vp++apa+f+pvrg Gsrvwdq+g+e++dfaGGiavnalGhahp++ +al+eqa klwh++n 
  NCBI__GCF_000013785.1:WP_011912810.1   8 VERADFDQVIVPTFAPAAFVPVRGLGSRVWDQSGRELVDFAGGIAVNALGHAHPAMIAALTEQAGKLWHISNI 80 
                                           79*********************************************************************** PP

                             TIGR03246  74 ytnepvlrlakklvdatfadkvffcnsGaeaneaalklarkvaldkygaekseivafknsfhGrtlftvsvGG 146
                                           ytnep+lrlakklv atfad++ffcnsGaeane+a+klar++a+d yg++k ei++  nsfhGrtlftv+vGG
  NCBI__GCF_000013785.1:WP_011912810.1  81 YTNEPALRLAKKLVAATFADRAFFCNSGAEANESAFKLARRYAHDVYGPQKFEIISALNSFHGRTLFTVTVGG 153
                                           ************************************************************************* PP

                             TIGR03246 147 qakysedfaplpegikhaayndlealkalisdktcavivepiqGegGvvpadkaflkglrelcdrhnallifd 219
                                           q+kys++f+p++egi+h++yndlealka+isdktcav++epiqGe+G++p ++a+l+g+r+lc++hnallifd
  NCBI__GCF_000013785.1:WP_011912810.1 154 QSKYSDGFGPKIEGITHVPYNDLEALKAAISDKTCAVVLEPIQGESGILPGEQAYLEGARQLCNEHNALLIFD 226
                                           ************************************************************************* PP

                             TIGR03246 220 evqtGvGrtGelyaymeyGvtpdiltsakalGgGfpiGalltteelakvlkvGthGttyGGnplacavaekvl 292
                                           evqtG+GrtGel+aym+yGvtpdilt ak+lGgGfpiGa+ltt+e+a++++vGthGttyGGnplacavae+vl
  NCBI__GCF_000013785.1:WP_011912810.1 227 EVQTGLGRTGELFAYMHYGVTPDILTNAKSLGGGFPIGAMLTTNEIAAHFSVGTHGTTYGGNPLACAVAETVL 299
                                           ************************************************************************* PP

                             TIGR03246 293 dlvntaelleGvkqrhelfvdelekinarykvfseirGkGlliGavlteeyaGkakdlvnaaaeeGvlvliaG 365
                                           d+vnt+e+leGvk+rhe+f ++l +i++ry vfs++rG+GlliG+vl+++++Gka  +  aa++e ++vl+aG
  NCBI__GCF_000013785.1:WP_011912810.1 300 DIVNTPEVLEGVKARHERFKARLLQIGERYGVFSQVRGRGLLIGCVLSDAWKGKAGAFWAAAEKEALMVLQAG 372
                                           ************************************************************************* PP

                             TIGR03246 366 pdvvrfapslvieeeeikeGlarlekavekl 396
                                           pdvvr+apsl+i+e++i+eGl+r+e+a+++l
  NCBI__GCF_000013785.1:WP_011912810.1 373 PDVVRLAPSLIIDEADIDEGLDRFERAIATL 403
                                           ****************************986 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: 00:00:00.00
# Mc/sec: 16.89
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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