GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Psychromonas ossibalaenae JAMM 0738

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_019615880.1 G327_RS0116355 acetate kinase

Query= BRENDA::E3W769
         (401 letters)



>NCBI__GCF_000381745.1:WP_019615880.1
          Length = 399

 Score =  511 bits (1316), Expect = e-149
 Identities = 251/400 (62%), Positives = 314/400 (78%), Gaps = 1/400 (0%)

Query: 1   MSDKLVLVLNCGSSSLKFAIIDAQSGDDKISGLAECFGLEDSRIKWKFNGGKNEAKLGAF 60
           MS+KLVLVLNCGSSSLKFA+I+A +GD+ ISGLAECF L D+R+KW  +G K+ A L   
Sbjct: 1   MSNKLVLVLNCGSSSLKFAVINANNGDEIISGLAECFNLPDARMKWNISGKKDAAHLPPN 60

Query: 61  TAHREAVEFFIVNNILAEHPELAAQIKAIGHRIVHGGEKFTRSVIITPEVIQGIEDCASL 120
           +AH EA+ + IV  I+     LA Q  A+GHR+VHGGEKFT SV+ITP+V + I++CASL
Sbjct: 61  SAHAEAISY-IVEEIIKNEQGLAEQFVAVGHRVVHGGEKFTESVVITPDVCKSIKECASL 119

Query: 121 APLHNPAHLIGIRAAIASFPQLPQVTVFDTAFHQTMPEKAYIYALPYKLYREHSIRRYGM 180
           APLHNPA ++GI+AA A+FP+LPQV VFDTAFHQTMP  A++YALPY LY+E  IRRYGM
Sbjct: 120 APLHNPAAIMGIKAARAAFPELPQVAVFDTAFHQTMPASAFLYALPYHLYKEKGIRRYGM 179

Query: 181 HGTSHFYVCREAAKVLGKDVKDINVICAHLGNGASVAAIKGGKSVDTSMGLTPLEGLVMG 240
           HGTSH +V REAA++L K + + NVI AHLGNG SV A+K GK VDTSMG+TPL GLVMG
Sbjct: 180 HGTSHLFVSREAARLLDKPLAETNVITAHLGNGGSVCAVKNGKCVDTSMGMTPLAGLVMG 239

Query: 241 TRCGDLDPSIIFHLVKQLGYTLDEVNNLLNKQSGLLGISELTNDCRGIEEGYHDGHKGAT 300
           TRCGD+DPSII HLV + GY+   V ++L KQSGLLGIS +++D R I+     G++ A 
Sbjct: 240 TRCGDIDPSIIEHLVAREGYSPAGVMDILQKQSGLLGISGVSSDFRDIQSACEKGNEQAI 299

Query: 301 LALDIFCYRLAKYIASYTVPLGRLDAIIFTGGIGENSNLIREKVLNLLEIFNFKVDDILN 360
           LA DIFCYRLAKYIA Y VPLGR+DA++FTGGIGENS ++R+KVLNLL +F ++VD   N
Sbjct: 300 LARDIFCYRLAKYIAGYAVPLGRIDALVFTGGIGENSAMVRDKVLNLLSVFGYQVDSEKN 359

Query: 361 KAARFGQQGVITQAGTPIAMVIPTNEEWVIAEDAIKLITA 400
           +    G++G IT   +P AMVIPTNEEWVIA+D+  L++A
Sbjct: 360 ETTILGKKGTITTENSPTAMVIPTNEEWVIAQDSASLVSA 399


Lambda     K      H
   0.321    0.139    0.409 

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: 523
Number of extensions: 28
Number of successful extensions: 2
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: 401
Length of database: 399
Length adjustment: 31
Effective length of query: 370
Effective length of database: 368
Effective search space:   136160
Effective search space used:   136160
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_019615880.1 G327_RS0116355 (acetate kinase)
to HMM TIGR00016 (ackA: acetate kinase (EC 2.7.2.1))

# 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/TIGR00016.hmm
# target sequence database:        /tmp/gapView.3886381.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00016  [M=405]
Accession:   TIGR00016
Description: ackA: acetate kinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.7e-163  528.6   0.0   5.2e-163  528.4   0.0    1.0  1  NCBI__GCF_000381745.1:WP_019615880.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000381745.1:WP_019615880.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  528.4   0.0  5.2e-163  5.2e-163       2     404 ..       2     397 ..       1     398 [. 0.97

  Alignments for each domain:
  == domain 1  score: 528.4 bits;  conditional E-value: 5.2e-163
                             TIGR00016   2 kskkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllnt 74 
                                           ++k++lvln+Gssslkfa+++a+n++++ +sgl+e+++l++ar+k+  +g+k  ++    ++h+ea++ ++++
  NCBI__GCF_000381745.1:WP_019615880.1   2 SNKLVLVLNCGSSSLKFAVINANNGDEI-ISGLAECFNLPDARMKWNISGKKDAAHLPPNSAHAEAISYIVEE 73 
                                           6799********************9998.9******************************************* PP

                             TIGR00016  75 lkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkak 147
                                           + k++  + + ++  ++GHRvvhGgekftesv++t +v k+ik+ ++lAPlHnpa++ gi+a+      ++ +
  NCBI__GCF_000381745.1:WP_019615880.1  74 IIKNE--QGLAEQFVAVGHRVVHGGEKFTESVVITPDVCKSIKECASLAPLHNPAAIMGIKAAR--AAFPELP 142
                                           *9754..6778899**************************************************..6677889 PP

                             TIGR00016 148 nvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasv 220
                                           +vavFDtafHqt+p  a+lYalPy+lyke+g+RrYG+HGtsh +v+++aa+ll+kpl++ n+i++HlGnG+sv
  NCBI__GCF_000381745.1:WP_019615880.1 143 QVAVFDTAFHQTMPASAFLYALPYHLYKEKGIRRYGMHGTSHLFVSREAARLLDKPLAETNVITAHLGNGGSV 215
                                           ************************************************************************* PP

                             TIGR00016 221 savknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdil 293
                                           +avknGk++dtsmG+tPL+GlvmGtR+GdiDp+ii +l  ++g s + + ++l+k+sGllgisg+ssD+Rdi 
  NCBI__GCF_000381745.1:WP_019615880.1 216 CAVKNGKCVDTSMGMTPLAGLVMGTRCGDIDPSIIEHLVAREGYSPAGVMDILQKQSGLLGISGVSSDFRDIQ 288
                                           ************************************************************************* PP

                             TIGR00016 294 dkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnn 366
                                           ++ e+gne+a lA +++++R+akyi+ y+  l g++Da+vFtgGiGen+a+vr++vl+ l v+G ++d+e+n+
  NCBI__GCF_000381745.1:WP_019615880.1 289 SACEKGNEQAILARDIFCYRLAKYIAGYAVPL-GRIDALVFTGGIGENSAMVRDKVLNLLSVFGYQVDSEKNE 360
                                           ********************************.67************************************** PP

                             TIGR00016 367 aarsgkesvisteeskvkvlviptneelviaeDalrla 404
                                           ++  gk++ i+te+s  +++viptnee+via+D++ l+
  NCBI__GCF_000381745.1:WP_019615880.1 361 TTILGKKGTITTENSP-TAMVIPTNEEWVIAQDSASLV 397
                                           ***********99998.5799************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (399 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 25.82
//
[ok]

This GapMind analysis is from Sep 24 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