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_019616529.1 G327_RS0119705 acetate kinase

Query= BRENDA::P63411
         (400 letters)



>NCBI__GCF_000381745.1:WP_019616529.1
          Length = 402

 Score =  557 bits (1435), Expect = e-163
 Identities = 277/403 (68%), Positives = 329/403 (81%), Gaps = 5/403 (1%)

Query: 1   MSSKLVLVLNCGSSSLKFAIIDAVNGDEYLSGLAECFHLPEARIKWKMDGSKQEAALGAG 60
           MS+KL+LVLNCGSSSLKFAIID  +GDE +SGLAEC HL +ARIKW ++G K  A LG G
Sbjct: 1   MSAKLILVLNCGSSSLKFAIIDTTSGDEKISGLAECLHLDDARIKWNLEGVKGSADLGTG 60

Query: 61  AAHSEALNFIVNTILAQKPELSAQLTAIGHRIVHGGEKYTSSVVIDESVIQGIKDSASFA 120
           AAH EALN+IV+ +L+QKPEL   L AIGHR+VHGGEK+TSSVVI + V++GI++  + A
Sbjct: 61  AAHEEALNYIVSELLSQKPELKENLFAIGHRVVHGGEKFTSSVVITDEVMKGIEECVALA 120

Query: 121 PLHNPAHLIGIAEALKSFPQLKDKNVAVFDTAFHQTMPEESYLYALPYSLYKEHGVRRYG 180
           PLHNPAHL+GI  A  +F  L   NVAVFDTAFHQTMPEE++LYALPY LY+E GVRRYG
Sbjct: 121 PLHNPAHLVGIRAAQHAFASLP--NVAVFDTAFHQTMPEEAFLYALPYKLYRESGVRRYG 178

Query: 181 AHGTSHFYVTQEAAKMLNKPVEELNIITCHLGNGGSVSAIRNGKCVDTSMGLTPLEGLVM 240
            HGTSH+Y++ +AA++LNKPV ELNII CHLGNGGSV AI+NG  VDTSMG+TPLEGLVM
Sbjct: 179 MHGTSHYYISLQAAEVLNKPVNELNIINCHLGNGGSVCAIKNGISVDTSMGMTPLEGLVM 238

Query: 241 GTRSGDIDPAIIFHLHDTLGMSVDQINKMLTKESGLLGLTEVTSDCRYVEDNYATKEDAK 300
           GTR GD+DPA+IFHLHD LG S+++IN MLTKESGLLGLTE TSDCR+VEDNY T   AK
Sbjct: 239 GTRCGDMDPAVIFHLHDELGYSLEEINTMLTKESGLLGLTEKTSDCRFVEDNYETDTAAK 298

Query: 301 RAMDVYCHRLAKYIGSYTALMDGRLDAVVFTGGIGENAAMVRELSLGKLGVLGFEVDHER 360
           RAMD+YC+RLAKYI SYTA +DGRLDAVVFTGGIGEN+A +R+L+L +L +LGF+V+ E 
Sbjct: 299 RAMDLYCYRLAKYIASYTAALDGRLDAVVFTGGIGENSAPIRKLTLERLSLLGFKVNEEA 358

Query: 361 NLAARFGK---SGFINKEGTRPAVVIPTNEELVIAQDASRLTA 400
           NLA RFGK    G I  E +  A+VI TNEE VIA D   L +
Sbjct: 359 NLANRFGKESNQGIITDENSTVAMVIQTNEEWVIAHDTLDLVS 401


Lambda     K      H
   0.318    0.134    0.384 

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: 514
Number of extensions: 11
Number of successful extensions: 3
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: 400
Length of database: 402
Length adjustment: 31
Effective length of query: 369
Effective length of database: 371
Effective search space:   136899
Effective search space used:   136899
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_019616529.1 G327_RS0119705 (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.4193429.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.4e-171  555.9   0.1   2.7e-171  555.7   0.1    1.0  1  NCBI__GCF_000381745.1:WP_019616529.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000381745.1:WP_019616529.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  555.7   0.1  2.7e-171  2.7e-171       2     404 ..       2     400 ..       1     401 [. 0.96

  Alignments for each domain:
  == domain 1  score: 555.7 bits;  conditional E-value: 2.7e-171
                             TIGR00016   2 kskkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllnt 74 
                                           + k+ilvln+Gssslkfa++d+++++++ +sgl+e+++l++arik+  +g k++++    ++heea++ ++++
  NCBI__GCF_000381745.1:WP_019616529.1   2 SAKLILVLNCGSSSLKFAIIDTTSGDEK-ISGLAECLHLDDARIKWNLEGVKGSADLGTGAAHEEALNYIVSE 73 
                                           6789********************9999.9******************************************* PP

                             TIGR00016  75 lkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkak 147
                                           l ++k   ++++++ +iGHRvvhGgekft+sv++tdev+k+i++ + lAPlHnpa+l gi+a++  +   + +
  NCBI__GCF_000381745.1:WP_019616529.1  74 LLSQK--PELKENLFAIGHRVVHGGEKFTSSVVITDEVMKGIEECVALAPLHNPAHLVGIRAAQ--HAFASLP 142
                                           **866..9999*****************************************************..6667788 PP

                             TIGR00016 148 nvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasv 220
                                           nvavFDtafHqt+peea+lYalPy+ly+e gvRrYG+HGtsh+y++ +aa++lnkp+++ln+i cHlGnG+sv
  NCBI__GCF_000381745.1:WP_019616529.1 143 NVAVFDTAFHQTMPEEAFLYALPYKLYRESGVRRYGMHGTSHYYISLQAAEVLNKPVNELNIINCHLGNGGSV 215
                                           ************************************************************************* PP

                             TIGR00016 221 savknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdil 293
                                           +a+knG s+dtsmG+tPLeGlvmGtR+Gd+Dpa+i++l+++lg sl+ei+++l+k+sGllg+++++sD+R ++
  NCBI__GCF_000381745.1:WP_019616529.1 216 CAIKNGISVDTSMGMTPLEGLVMGTRCGDMDPAVIFHLHDELGYSLEEINTMLTKESGLLGLTEKTSDCRFVE 288
                                           ************************************************************************* PP

                             TIGR00016 294 dkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnn 366
                                           d++ e++  ak+A+++y++R+akyi++y+a+l+g+lDa+vFtgGiGen+a +r+l+le+l +lG+k+++e n 
  NCBI__GCF_000381745.1:WP_019616529.1 289 DNY-ETDTAAKRAMDLYCYRLAKYIASYTAALDGRLDAVVFTGGIGENSAPIRKLTLERLSLLGFKVNEEANL 360
                                           ***.9999***************************************************************** PP

                             TIGR00016 367 aarsgkes...visteeskvkvlviptneelviaeDalrla 404
                                           a r+gkes   +i+ e+s+v ++vi+tnee+via+D+l l+
  NCBI__GCF_000381745.1:WP_019616529.1 361 ANRFGKESnqgIITDENSTV-AMVIQTNEEWVIAHDTLDLV 400
                                           99888764332677666665.789************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (402 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: 27.77
//
[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