Alignments for a candidate for ackA in Herbaspirillum autotrophicum IAM 14942

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Herbaspirillum autotrophicum IAM 14942

Align Acetate kinase; EC 2.7.2.1; Acetokinase (uncharacterized)
to candidate WP_050461168.1 AKL27_RS02525 acetate/propionate family kinase

Query= curated2:Q6N143
         (398 letters)



>NCBI__GCF_001189915.1:WP_050461168.1
          Length = 399

 Score =  343 bits (880), Expect = 5e-99
 Identities = 197/397 (49%), Positives = 251/397 (63%), Gaps = 9/397 (2%)

Query: 1   MSDVLLVLNAGSSSIKFALYEAHTEPTADHLICEGGIGSLGHRPHFKVVNSDGSTRYDTY 60
           M++++LVLN GSSSIKF L+EA  E  A   I  G    +G   H  V+   GS      
Sbjct: 1   MNELILVLNCGSSSIKFGLFEAGPEQLARQAIWRGKADGIGS--HNAVLEIHGSATSALT 58

Query: 61  LPEGTSHDDAMAVLIGWIET--TFPEHRLSAVGHRVVHGGALFDGPVDVTPEVIAQLRAF 118
           L     + DA+  +   +    T    RL ++ HRVVHGGA +  PV V   V+  LR++
Sbjct: 59  LSAENPYHDALGAIRTEVLAYLTHTGSRLLSIAHRVVHGGAKYFAPVRVDHAVLEDLRSY 118

Query: 119 DRLAPLHQPHNVSAIEALAKLHPSLPQIACFDTAFHHRLPEVATAFALPRELTEQGVRRY 178
             LAPLHQP  + AIEAL   HP LPQ+ACFDTAFHH +P V     LP+   ++G+RRY
Sbjct: 119 IPLAPLHQPFALEAIEALLNSHPELPQVACFDTAFHHTVPRVEQMLPLPQAAWDRGLRRY 178

Query: 179 GFHGLSYEYIAGRLPDVAGQAVADGRVVVAHLGAGASMCAMLRCRSIATTMGFTALDGLM 238
           GFHGLSYEY +  L +  G A A G+ +VAHLG+GAS+CAM   RS+ATTMGF+ALDGLM
Sbjct: 179 GFHGLSYEYQSLVLAERYGDA-ARGKTIVAHLGSGASLCAMQDLRSVATTMGFSALDGLM 237

Query: 239 MGSRCGELDPGVVLYLLEEKSMTAREIEDLLYRESGLLGVSGISDDMRTLL--ASDDPHA 296
           MG+RCG LDPG VLYLLE +  T ++I  LLYRESGLLGVSG+S D R LL    D+P  
Sbjct: 238 MGTRCGTLDPGAVLYLLEIEKQTPQQIGQLLYRESGLLGVSGVSSDPRILLQQEQDNPAV 297

Query: 297 CEAIELFVYRIARELGSLAAALGGLDALVFTGGIGEHASEIRRRVCEQAAWLGVTLDPDA 356
            +A++L+V RI RE+G+L A LGGLD LVFT GIGE+ +EIR R+C    +LG+ LD  A
Sbjct: 298 RDALDLYVRRIVREIGALTAVLGGLDLLVFTAGIGENNAEIRSRICHALCFLGIGLDNVA 357

Query: 357 NASLSGAGRISAPDSKVSAWAIPTDEDLMIARHVWRL 393
           NA    A  IS    +       T+E+ + A H  +L
Sbjct: 358 NA--GNAAVISRSGRQPLVAVEATNEEWIAASHARQL 392


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: 461
Number of extensions: 18
Number of successful extensions: 4
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: 399
Length adjustment: 31
Effective length of query: 367
Effective length of database: 368
Effective search space:   135056
Effective search space used:   135056
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_050461168.1 AKL27_RS02525 (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.3277593.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.6e-107  344.1   0.0   5.2e-107  344.0   0.0    1.0  1  NCBI__GCF_001189915.1:WP_050461168.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001189915.1:WP_050461168.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  344.0   0.0  5.2e-107  5.2e-107       4     403 ..       3     392 ..       1     394 [. 0.93

  Alignments for each domain:
  == domain 1  score: 344.0 bits;  conditional E-value: 5.2e-107
                             TIGR00016   4 kkilvlnaGssslkfalldaen...sekvllsglverikleeariktvedgekkeeeklaiedheeavkklln 73 
                                           ++ilvln+Gsss+kf l++a     +++ +++g ++ i +++a+   ++ + +   +  a + ++ a+ ++ +
  NCBI__GCF_001189915.1:WP_050461168.1   3 ELILVLNCGSSSIKFGLFEAGPeqlARQAIWRGKADGIGSHNAV-LEIHGSATSALTLSAENPYHDALGAIRT 74 
                                           78*****************9743345566**************5.556666677888889999********** PP

                             TIGR00016  74 tlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllka 146
                                           ++ +   ++++ s +  i HRvvhGg k+   v v++ vl++++  ++lAPlH p +le+iea+l  + +++ 
  NCBI__GCF_001189915.1:WP_050461168.1  75 EVLA--YLTHTGSRLLSIAHRVVHGGAKYFAPVRVDHAVLEDLRSYIPLAPLHQPFALEAIEALL--NSHPEL 143
                                           *996..7899*******************************************************..899999 PP

                             TIGR00016 147 knvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGas 219
                                           ++va+FDtafH+t+p+   + +lP+ ++ + g+RrYGfHG+s++y +  +a+  +  ++  + iv+HlG Gas
  NCBI__GCF_001189915.1:WP_050461168.1 144 PQVACFDTAFHHTVPRVEQMLPLPQAAW-DRGLRRYGFHGLSYEYQSLVLAERYGD-AARGKTIVAHLGSGAS 214
                                           ************************6666.679***********************9.778899********** PP

                             TIGR00016 220 vsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdi 292
                                           ++a+++ +s+ t+mG+  L+Gl+mGtR+G +Dp+++ yl e ++++ ++i ++l ++sGllg+sg+ssD R +
  NCBI__GCF_001189915.1:WP_050461168.1 215 LCAMQDLRSVATTMGFSALDGLMMGTRCGTLDPGAVLYLLEIEKQTPQQIGQLLYRESGLLGVSGVSSDPRIL 287
                                           ************************************************************************* PP

                             TIGR00016 293 ldkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldleln 365
                                           l++  + n   + Al++yv Ri + ig+ +a l g lD +vFt+GiGen+ae+r +++++l +lG+ ld+  n
  NCBI__GCF_001189915.1:WP_050461168.1 288 LQQE-QDNPAVRDALDLYVRRIVREIGALTAVLGG-LDLLVFTAGIGENNAEIRSRICHALCFLGIGLDNVAN 358
                                           9998.8999************************76.*********************************8877 PP

                             TIGR00016 366 naarsgkesvisteeskvkvlviptneelviaeDalrl 403
                                                g+ +vis +  +  v+v  tnee++ a  a +l
  NCBI__GCF_001189915.1:WP_050461168.1 359 A----GNAAVISRSGRQPLVAVEATNEEWIAASHARQL 392
                                           7....999****998888899999*****999877666 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 15.92
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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