GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astC in Klebsiella michiganensis M5al

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate BWI76_RS11670 BWI76_RS11670 aspartate aminotransferase family protein

Query= reanno::Koxy:BWI76_RS11670
         (406 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS11670 BWI76_RS11670 aspartate
           aminotransferase family protein
          Length = 406

 Score =  818 bits (2113), Expect = 0.0
 Identities = 406/406 (100%), Positives = 406/406 (100%)

Query: 1   MSQSITRSNFDEWMMPVYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRL 60
           MSQSITRSNFDEWMMPVYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRL
Sbjct: 1   MSQSITRSNFDEWMMPVYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRL 60

Query: 61  VKALTEQAGKFWHTGNGYTNEPVLRLAKQLIDATFADRVFFCNSGAEANEAALKLARKYA 120
           VKALTEQAGKFWHTGNGYTNEPVLRLAKQLIDATFADRVFFCNSGAEANEAALKLARKYA
Sbjct: 61  VKALTEQAGKFWHTGNGYTNEPVLRLAKQLIDATFADRVFFCNSGAEANEAALKLARKYA 120

Query: 121 HDRFGSEKSGIVAFKNAFHGRTLFTVSAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKALI 180
           HDRFGSEKSGIVAFKNAFHGRTLFTVSAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKALI
Sbjct: 121 HDRFGSEKSGIVAFKNAFHGRTLFTVSAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKALI 180

Query: 181 DDNTCAVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMH 240
           DDNTCAVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMH
Sbjct: 181 DDNTCAVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMH 240

Query: 241 YGVTPDLLSTAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATIN 300
           YGVTPDLLSTAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATIN
Sbjct: 241 YGVTPDLLSTAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATIN 300

Query: 301 TREVLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAAE 360
           TREVLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAAE
Sbjct: 301 TREVLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAAE 360

Query: 361 EGLMILIAGANVVRFAPALIISEDEVNSGLDRFELACKRFLAGVSS 406
           EGLMILIAGANVVRFAPALIISEDEVNSGLDRFELACKRFLAGVSS
Sbjct: 361 EGLMILIAGANVVRFAPALIISEDEVNSGLDRFELACKRFLAGVSS 406


Lambda     K      H
   0.321    0.137    0.412 

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: 708
Number of extensions: 19
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 BWI76_RS11670 BWI76_RS11670 (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.16241.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   3.2e-228  743.3   0.2   3.7e-228  743.1   0.2    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS11670  BWI76_RS11670 aspartate aminotra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS11670  BWI76_RS11670 aspartate aminotransferase family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  743.1   0.2  3.7e-228  3.7e-228       1     396 [.       5     400 ..       5     401 .. 1.00

  Alignments for each domain:
  == domain 1  score: 743.1 bits;  conditional E-value: 3.7e-228
                               TIGR03246   1 veresfdevmvpvyapakfipvrgeGsrvwdqegkeyidfaGGiavnalGhahpelvealkeqaeklwhlg 71 
                                             ++r++fde+m+pvyapa+fipvrgeGsr+wdq+gkeyidfaGGiavnalGhahp lv+al+eqa k+wh+g
  lcl|FitnessBrowser__Koxy:BWI76_RS11670   5 ITRSNFDEWMMPVYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWHTG 75 
                                             79********************************************************************* PP

                               TIGR03246  72 ngytnepvlrlakklvdatfadkvffcnsGaeaneaalklarkvaldkygaekseivafknsfhGrtlftv 142
                                             ngytnepvlrlak+l+datfad+vffcnsGaeaneaalklark+a+d++g+eks ivafkn+fhGrtlftv
  lcl|FitnessBrowser__Koxy:BWI76_RS11670  76 NGYTNEPVLRLAKQLIDATFADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVAFKNAFHGRTLFTV 146
                                             *********************************************************************** PP

                               TIGR03246 143 svGGqakysedfaplpegikhaayndlealkalisdktcavivepiqGegGvvpadkaflkglrelcdrhn 213
                                             s+GGq++ys+dfaplp +i+ha+yndl+++kali+d+tcavivep+qGegGvvpad +fl+glrelcd+hn
  lcl|FitnessBrowser__Koxy:BWI76_RS11670 147 SAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKALIDDNTCAVIVEPMQGEGGVVPADADFLRGLRELCDAHN 217
                                             *********************************************************************** PP

                               TIGR03246 214 allifdevqtGvGrtGelyaymeyGvtpdiltsakalGgGfpiGalltteelakvlkvGthGttyGGnpla 284
                                             allifdevqtGvGrtGelyaym+yGvtpd+l++akalGgGfpiGall++e++a+v++vGthGttyGGnpla
  lcl|FitnessBrowser__Koxy:BWI76_RS11670 218 ALLIFDEVQTGVGRTGELYAYMHYGVTPDLLSTAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLA 288
                                             *********************************************************************** PP

                               TIGR03246 285 cavaekvldlvntaelleGvkqrhelfvdelekinarykvfseirGkGlliGavlteeyaGkakdlvnaaa 355
                                             cava++v+ ++nt e+l+Gvkqrh++f ++l++inary +f+eirG GlliG+vl++eyaGkak + n+aa
  lcl|FitnessBrowser__Koxy:BWI76_RS11670 289 CAVAGEVFATINTREVLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAA 359
                                             *********************************************************************** PP

                               TIGR03246 356 eeGvlvliaGpdvvrfapslvieeeeikeGlarlekavekl 396
                                             eeG+++liaG++vvrfap+l+i+e+e++ Gl+r+e a++++
  lcl|FitnessBrowser__Koxy:BWI76_RS11670 360 EEGLMILIAGANVVRFAPALIISEDEVNSGLDRFELACKRF 400
                                             **************************************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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.88
//
[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:

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 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