Alignments for a candidate for ackA in Brucella inopinata BO1

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.1827367.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 17.41
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources