GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Brucella inopinata BO1

Align Acetate kinase; EC 2.7.2.1; Acetokinase (uncharacterized)
to candidate WP_008509973.1 BIBO1_RS16460 acetate/propionate family kinase

Query= curated2:Q6N143
         (398 letters)



>NCBI__GCF_000182725.1:WP_008509973.1
          Length = 401

 Score =  302 bits (773), Expect = 1e-86
 Identities = 165/397 (41%), Positives = 247/397 (62%), Gaps = 13/397 (3%)

Query: 1   MSDVLLVLNAGSSSIKFALYEAHTEPTADHLICEGGIGSLGHRPHFKVVNSDGSTRYDTY 60
           M+  L+  NAGSS++K  ++E   +  A   + +G I   G    F++   +G+   D  
Sbjct: 1   MNKQLVTFNAGSSTVKIGVFEC--DGNAARKVSKGDIDLTGSPLRFRLRGENGNL--DIV 56

Query: 61  LPEGTSHDDAMAVLIGWIETTFPEH----RLSAVGHRVVHGGALFDGPVDVTPEVIAQLR 116
           L    S  D +  ++G +     EH    R+ AVGHRVV GG  F   V +  + +  + 
Sbjct: 57  L--SASGTDDITTILGELFDRLAEHIDPSRILAVGHRVVFGGDDFAQAVLIDDDNLEAIE 114

Query: 117 AFDRLAPLHQPHNVSAIEALAKLHPSLPQIACFDTAFHHRLPEVATAFALPRELTEQGVR 176
                APLHQP +++ I+A+ K+ P L Q A FDTAFH  +P+    FA+P+EL ++G++
Sbjct: 115 RLSIFAPLHQPKSLALIKAVRKIFPHLAQTASFDTAFHQTIPDTVRRFAIPQELHDRGIK 174

Query: 177 RYGFHGLSYEYIAGRLPDVAGQAVADGRVVVAHLGAGASMCAMLRCRSIATTMGFTALDG 236
           R+GFHGLSY+ I G     A + +A+G+++ AHLG+GAS+CAM + +S+ T+M F+ LDG
Sbjct: 175 RFGFHGLSYKSIIGNFSQRAPE-LAEGKIIAAHLGSGASLCAMHKRKSLDTSMSFSTLDG 233

Query: 237 LMMGSRCGELDPGVVLYLLEEKSMTAREIEDLLYRESGLLGVSGISDDMRTLLASDDPHA 296
           + M +RCG LDPGV+L+LL+++ M +  + DLLY  SGLLG+SG+S D R LL SD P A
Sbjct: 234 IPMATRCGALDPGVLLHLLQQEKMESDALADLLYHRSGLLGLSGLSGDTRDLLESDAPQA 293

Query: 297 CEAIELFVYRIARELGSLAAALGGLDALVFTGGIGEHASEIRRRVCEQAAWLGVTLDPDA 356
             A+++F  RIA E+  LA+ L GLDA++FT GIGEH   IR  +C++ AW GV LDP A
Sbjct: 294 RAALDIFALRIAGEICRLASTLNGLDAVIFTAGIGEHQPAIRAAICQRLAWQGVELDPAA 353

Query: 357 NASLSGAGRISAPDSKVSAWAIPTDEDLMIARHVWRL 393
           N     A  I++  S+ +A+ +PTDE+ +IA   + +
Sbjct: 354 ND--ENAFCITSRTSRTAAFVLPTDEEQIIASETFEI 388


Lambda     K      H
   0.321    0.137    0.413 

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: 421
Number of extensions: 15
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: 398
Length of database: 401
Length adjustment: 31
Effective length of query: 367
Effective length of database: 370
Effective search space:   135790
Effective search space used:   135790
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate WP_008509973.1 BIBO1_RS16460 (acetate/propionate family 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.3317766.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    5.9e-96  307.6   0.0    6.7e-96  307.4   0.0    1.0  1  NCBI__GCF_000182725.1:WP_008509973.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000182725.1:WP_008509973.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  307.4   0.0   6.7e-96   6.7e-96       4     403 ..       3     388 ..       1     390 [. 0.91

  Alignments for each domain:
  == domain 1  score: 307.4 bits;  conditional E-value: 6.7e-96
                             TIGR00016   4 kkilvlnaGssslkfalldaen.sekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntl 75 
                                           k+++  naGss +k  +++  + + +++ +g ++ + ++  +      ge+++ +++  ++ +  ++++l +l
  NCBI__GCF_000182725.1:WP_008509973.1   3 KQLVTFNAGSSTVKIGVFECDGnAARKVSKGDIDLTGSPLRF---RLRGENGNLDIVLSASGTDDITTILGEL 72 
                                           567789*************98635666789988887777664...4577777888888888888888888888 PP

                             TIGR00016  76 kkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkakn 148
                                            +  + + + s i ++GHRvv Gg++f+++v+++d+ l++i+++s +APlH p  l  i+av k++  ++  +
  NCBI__GCF_000182725.1:WP_008509973.1  73 FDRLAEHIDPSRILAVGHRVVFGGDDFAQAVLIDDDNLEAIERLSIFAPLHQPKSLALIKAVRKIF--PHLAQ 143
                                           876666778899***************************************************555..5556* PP

                             TIGR00016 149 vavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvs 221
                                            a FDtafHqtip+    +a+P++l ++ g++r+GfHG+s+k +  + ++     l++ ++i +HlG Gas++
  NCBI__GCF_000182725.1:WP_008509973.1 144 TASFDTAFHQTIPDTVRRFAIPQEL-HDRGIKRFGFHGLSYKSIIGNFSQRAPE-LAEGKIIAAHLGSGASLC 214
                                           **********************665.689*************999988888766.899*************** PP

                             TIGR00016 222 avknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdild 294
                                           a+++ ks+dtsm +  L+G+ m tR+G +Dp+++ +l +++++  d++ ++l  +sGllg+sgls D Rd+l+
  NCBI__GCF_000182725.1:WP_008509973.1 215 AMHKRKSLDTSMSFSTLDGIPMATRCGALDPGVLLHLLQQEKMESDALADLLYHRSGLLGLSGLSGDTRDLLE 287
                                           ***********************************************************************99 PP

                             TIGR00016 295 kkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnna 367
                                                  +a+ Al++++ Ria  i + +++l+g lDa++Ft+GiGe +  +r+ ++++l+  G++ld++ n  
  NCBI__GCF_000182725.1:WP_008509973.1 288 SD---APQARAALDIFALRIAGEICRLASTLNG-LDAVIFTAGIGEHQPAIRAAICQRLAWQGVELDPAAND- 355
                                           87...6789**********************88.***********************************999. PP

                             TIGR00016 368 arsgkesvisteeskvkvlviptneelviaeDalrl 403
                                              ++   i+++ s++ ++v+pt+ee +ia +++++
  NCBI__GCF_000182725.1:WP_008509973.1 356 ---ENAFCITSRTSRTAAFVLPTDEEQIIASETFEI 388
                                           ...67778999*******************998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (401 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 18.58
//
[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