Alignments for a candidate for ackA in Rhodococcus qingshengii djl-6-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Rhodococcus qingshengii djl-6-2

Align Acetate kinase; Acetokinase; EC 2.7.2.1 (characterized)
to candidate WP_054186925.1 C1M55_RS07470 acetate kinase

Query= SwissProt::P77845
         (397 letters)



>NCBI__GCF_002893965.1:WP_054186925.1
          Length = 399

 Score =  455 bits (1171), Expect = e-133
 Identities = 232/389 (59%), Positives = 288/389 (74%), Gaps = 3/389 (0%)

Query: 5   LVLNSGSSSIKFQLVNPENSAIDEPYVSGLVEQIGEPNGRIVLKIEGEKYTLETPIADHS 64
           LV+NSGSSSIKFQLV+P+ +   E    GL+E+IGEP+G IV            PIADH 
Sbjct: 7   LVINSGSSSIKFQLVHPDTA---ESVAHGLIERIGEPDGHIVYNHRTGVEDRSLPIADHR 63

Query: 65  EGLNLAFDLMDQHNCGPSQLEITAVGHRVVHGGILFSAPELITDEIVEMIRDLIPLAPLH 124
            GL +  D++ +     S+  I AVGHRVVHGG +F +P LI D +V+ I DL  LAPLH
Sbjct: 64  AGLKMVLDIVAEVGRPLSEAGIIAVGHRVVHGGDIFYSPTLIDDGVVKAIADLSNLAPLH 123

Query: 125 NPANVDGIDVARKILPDVPHVAVFDTGFFHSLPPAAALYAINKDVAAEHGIRRYGFHGTS 184
           NPANV GI+VAR+ LPDVPHVAVFDT FFH+LP AA+ YAI++DVA  + IRRYGFHGTS
Sbjct: 124 NPANVIGIEVAREELPDVPHVAVFDTAFFHTLPAAASTYAIDRDVAKANQIRRYGFHGTS 183

Query: 185 HEFVSKRVVEILEKPTEDINTITFHLGNGASMAAVQGGRAVDTSMGMTPLAGLVMGTRSG 244
           HE+VS RV E L K   ++N I  HLGNGAS +A++GG+A+DT+MG+TPL GLVMGTRSG
Sbjct: 184 HEYVSGRVAEFLGKDPAELNQIVLHLGNGASASAIKGGKAIDTTMGLTPLEGLVMGTRSG 243

Query: 245 DIDPGIVFHLSRTAGMSIDEIDNLLNKKSGVKGLSGVNDFRELREMIDNNDQDAWSAYNI 304
           DIDPGI+ HL+R +GM +DEID+LLN++SG+KGLSGVNDFR L  +I+  DQDA  AY++
Sbjct: 244 DIDPGIILHLNRNSGMKVDEIDDLLNRRSGLKGLSGVNDFRALLALIEGGDQDAQLAYDV 303

Query: 305 YIHQLRRYLGSYMVALGRVDTIVFTAGVGENAQFVREDALAGLEMYGIEIDPERNALPND 364
           Y+H LR+Y+G+++V LG VD I FT GVGEN   VR D+LAGL   GIE+DP  N   N 
Sbjct: 304 YVHMLRKYIGAFIVQLGGVDVITFTGGVGENNIDVRRDSLAGLSRLGIEVDPALNEAKNR 363

Query: 365 GPRLISTDASKVKVFVIPTNEELAIARYA 393
             R IS  +S V+V V+PTNEELAIAR A
Sbjct: 364 DERRISASSSAVEVLVVPTNEELAIARAA 392


Lambda     K      H
   0.318    0.137    0.395 

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: 526
Number of extensions: 18
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: 397
Length of database: 399
Length adjustment: 31
Effective length of query: 366
Effective length of database: 368
Effective search space:   134688
Effective search space used:   134688
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_054186925.1 C1M55_RS07470 (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.4049674.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.8e-138  447.6   0.0     2e-138  447.4   0.0    1.0  1  NCBI__GCF_002893965.1:WP_054186925.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002893965.1:WP_054186925.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  447.4   0.0    2e-138    2e-138       3     403 ..       3     395 ..       1     397 [. 0.95

  Alignments for each domain:
  == domain 1  score: 447.4 bits;  conditional E-value: 2e-138
                             TIGR00016   3 skkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntl 75 
                                           +  +lv+n+Gsss+kf+l++  ++e+v ++gl+eri  ++ +i   + +   e   l i+dh++++k++l+ +
  NCBI__GCF_002893965.1:WP_054186925.1   3 DGTVLVINSGSSSIKFQLVHPDTAESV-AHGLIERIGEPDGHIVYNHRT-GVEDRSLPIADHRAGLKMVLDIV 73 
                                           5679******************88887.**********99966644433.45667899************999 PP

                             TIGR00016  76 kkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkakn 148
                                             +     +++ i ++GHRvvhGg+ f + ++++d v+k+i+d+s+lAPlHnpa+++gie +   ++l+++++
  NCBI__GCF_002893965.1:WP_054186925.1  74 A-EVGRPLSEAGIIAVGHRVVHGGDIFYSPTLIDDGVVKAIADLSNLAPLHNPANVIGIEVAR--EELPDVPH 143
                                           9.5777788889**************************************************9..9******* PP

                             TIGR00016 149 vavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvs 221
                                           vavFDtaf +t+p  a  Ya+ +++ k +++RrYGfHGtsh+yv+ r+a+ l+k  ++ln iv+HlGnGas s
  NCBI__GCF_002893965.1:WP_054186925.1 144 VAVFDTAFFHTLPAAASTYAIDRDVAKANQIRRYGFHGTSHEYVSGRVAEFLGKDPAELNQIVLHLGNGASAS 216
                                           ************************************************************************* PP

                             TIGR00016 222 avknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdild 294
                                           a+k Gk+idt+mGltPLeGlvmGtRsGdiDp+ii +l+ + g+ +dei ++ln++sGl g+sg  +D+R +l+
  NCBI__GCF_002893965.1:WP_054186925.1 217 AIKGGKAIDTTMGLTPLEGLVMGTRSGDIDPGIILHLNRNSGMKVDEIDDLLNRRSGLKGLSG-VNDFRALLA 288
                                           ***************************************************************.89******* PP

                             TIGR00016 295 kkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnna 367
                                            +e g+++a+lA++vyvh ++kyig++i +l g +D i FtgG+Gen+ +vr+++l +l  lG+++d++ln+ 
  NCBI__GCF_002893965.1:WP_054186925.1 289 LIEGGDQDAQLAYDVYVHMLRKYIGAFIVQLGG-VDVITFTGGVGENNIDVRRDSLAGLSRLGIEVDPALNE- 359
                                           *******************************76.**************************************. PP

                             TIGR00016 368 arsgkesvisteeskvkvlviptneelviaeDalrl 403
                                           a++ +e+ is + s+v+vlv+ptneel+ia+ a  l
  NCBI__GCF_002893965.1:WP_054186925.1 360 AKNRDERRISASSSAVEVLVVPTNEELAIARAAKAL 395
                                           9999**************************987655 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: 15.02
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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