Alignments for a candidate for ackA in Luteimonas huabeiensis HB2

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Luteimonas huabeiensis HB2

Align Acetate kinase; EC 2.7.2.1; Acetokinase (uncharacterized)
to candidate WP_024889080.1 Z164_RS0102040 acetate/propionate family kinase

Query= curated2:Q6N143
         (398 letters)



>NCBI__GCF_000559025.1:WP_024889080.1
          Length = 433

 Score =  358 bits (919), Expect = e-103
 Identities = 199/395 (50%), Positives = 257/395 (65%), Gaps = 8/395 (2%)

Query: 3   DVLLVLNAGSSSIKFALYEAHTEPTADHLICEGGIGSLGH-RPHFKVVNSDGSTRYDTYL 61
           +++LVLN GSSSIKFAL++A  +P     +  G +  +G   P F      G       L
Sbjct: 44  ELILVLNCGSSSIKFALFDAGRDPLPRAPVWNGKVQGIGGPSPTF---GETGVAPAPVAL 100

Query: 62  PEGTSHDDAMAVLIGWIETTFPEHRLSAVGHRVVHGGALFDGPVDVTPEVIAQLRAFDRL 121
                H  A+A +   +       RL +V HRVVHGG+ +  PV V   V+A L+++  L
Sbjct: 101 DAARPHHAALARIRERVLARLGGRRLHSVAHRVVHGGSRYFAPVRVDAGVLADLKSYVPL 160

Query: 122 APLHQPHNVSAIEALAKLHPSLPQIACFDTAFHHRLPEVATAFALPRELTEQGVRRYGFH 181
           APLHQP  + A+E L +  P+LPQ+ACFDTAFHH  P+V     LP    E+G+RRYGFH
Sbjct: 161 APLHQPFALEAMEILLRERPALPQVACFDTAFHHTRPQVEQLLPLPYAAWERGLRRYGFH 220

Query: 182 GLSYEYIAGRLPDVAGQAVADGRVVVAHLGAGASMCAMLRCRSIATTMGFTALDGLMMGS 241
           GLSYEY+A  LP+  G+A+A GR +VAHLG+GAS+CAM   +S+ATTMGF+ALDGLMMG+
Sbjct: 221 GLSYEYMAAALPERHGEALARGRTIVAHLGSGASLCAMRELQSVATTMGFSALDGLMMGT 280

Query: 242 RCGELDPGVVLYLLEEKSMTAREIEDLLYRESGLLGVSGISDDMRTLLASD--DPHACEA 299
           R G LDPG VLYL+E + ++  ++  +LY ESGLLGVSGIS D R LLA +   P A  A
Sbjct: 281 RTGALDPGAVLYLMEIEKLSLEQVARVLYHESGLLGVSGISADPRELLAREAGAPRAALA 340

Query: 300 IELFVYRIARELGSLAAALGGLDALVFTGGIGEHASEIRRRVCEQAAWLGVTLDPDANAS 359
           ++L+V RI RELG+LAA LGGLD LVFT GIGEH++ +R RVC Q  WLGV LD  ANA 
Sbjct: 341 LQLYVRRIVRELGALAAVLGGLDLLVFTAGIGEHSAVLRERVCAQLGWLGVALDAAANA- 399

Query: 360 LSGAGRISAPDSKVSAWAIPTDEDLMIARHVWRLA 394
            + A  ISA  S+V     PT+E+ + A H   LA
Sbjct: 400 -ADAPTISAAGSRVRVGVEPTNEEWIAAGHARGLA 433


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: 525
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: 433
Length adjustment: 31
Effective length of query: 367
Effective length of database: 402
Effective search space:   147534
Effective search space used:   147534
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_024889080.1 Z164_RS0102040 (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.3803220.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.7e-103  330.4   0.0   8.4e-103  330.1   0.0    1.0  1  NCBI__GCF_000559025.1:WP_024889080.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000559025.1:WP_024889080.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  330.1   0.0  8.4e-103  8.4e-103       4     397 ..      44     426 ..      41     432 .. 0.93

  Alignments for each domain:
  == domain 1  score: 330.1 bits;  conditional E-value: 8.4e-103
                             TIGR00016   4 kkilvlnaGssslkfalldaen...sekvllsglverikleeariktvedgekkeeeklaiedheeavkklln 73 
                                           ++ilvln+Gsss+kfal+da     ++  +++g v+ i  +  +    +       +  a + h++a++++ +
  NCBI__GCF_000559025.1:WP_024889080.1  44 ELILVLNCGSSSIKFALFDAGRdplPRAPVWNGKVQGIGGPSPTFG-ETGVAPAPVALDAARPHHAALARIRE 115
                                           689****************986566667799999999999988444.33333456677788899********* PP

                             TIGR00016  74 tlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllka 146
                                           ++ +    +     ++ + HRvvhGg+++   v v++ vl+++k  ++lAPlH p +le++e++l   + +  
  NCBI__GCF_000559025.1:WP_024889080.1 116 RVLA----RLGGRRLHSVAHRVVHGGSRYFAPVRVDAGVLADLKSYVPLAPLHQPFALEAMEILL--RERPAL 182
                                           9997....556788999***********************************************9..889999 PP

                             TIGR00016 147 knvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGas 219
                                           ++va+FDtafH+t p+   l +lPy +++  g+RrYGfHG+s++y++  + +  + +l+  + iv+HlG Gas
  NCBI__GCF_000559025.1:WP_024889080.1 183 PQVACFDTAFHHTRPQVEQLLPLPYAAWE-RGLRRYGFHGLSYEYMAAALPERHGEALARGRTIVAHLGSGAS 254
                                           9************************9996.69***************************************** PP

                             TIGR00016 220 vsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdi 292
                                           ++a+++ +s+ t+mG+  L+Gl+mGtR+G +Dp+++ yl+e ++lsl+++ ++l  +sGllg+sg+s+D R++
  NCBI__GCF_000559025.1:WP_024889080.1 255 LCAMRELQSVATTMGFSALDGLMMGTRTGALDPGAVLYLMEIEKLSLEQVARVLYHESGLLGVSGISADPREL 327
                                           ************************************************************************* PP

                             TIGR00016 293 ldkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldleln 365
                                           l++  +g  +a+lAl++yv Ri + +g+ +a l g lD +vFt+GiGe +a +re+v+ +l  lG++ld + n
  NCBI__GCF_000559025.1:WP_024889080.1 328 LARE-AGAPRAALALQLYVRRIVRELGALAAVLGG-LDLLVFTAGIGEHSAVLRERVCAQLGWLGVALDAAAN 398
                                           *998.9999************************76.**********************************999 PP

                             TIGR00016 366 naarsgkesvisteeskvkvlviptneelvia 397
                                                 +   is   s+v+v v ptnee++ a
  NCBI__GCF_000559025.1:WP_024889080.1 399 A----ADAPTISAAGSRVRVGVEPTNEEWIAA 426
                                           8....78899******************9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (433 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: 15.44
//
[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 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