GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Koxy:BWI76_RS11670
          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.16341.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 6.45
//
[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:

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