Alignments for a candidate for ackA in Mycolicibacterium vanbaalenii PYR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Mycolicibacterium vanbaalenii PYR-1

Align Acetate kinase; Acetokinase; EC 2.7.2.1 (characterized)
to candidate WP_011777976.1 MVAN_RS03540 acetate kinase

Query= SwissProt::P77845
         (397 letters)



>NCBI__GCF_000015305.1:WP_011777976.1
          Length = 389

 Score =  397 bits (1021), Expect = e-115
 Identities = 199/387 (51%), Positives = 264/387 (68%), Gaps = 16/387 (4%)

Query: 5   LVLNSGSSSIKFQLVNPENSAIDEPYVSGLVEQIGEPNGRIVLKIEGEKYTLETPIADHS 64
           LVLNSGSSS+K+ ++ P++  +      G+VE+IGE                E  + DH+
Sbjct: 6   LVLNSGSSSVKYAVLEPDSGVL---VADGIVERIGEEGA-------------ERAVTDHA 49

Query: 65  EGLNLAFDLMDQHNCGPSQLEITAVGHRVVHGGILFSAPELITDEIVEMIRDLIPLAPLH 124
             + + FD +         L + AVGHRVVHGG     P ++ D  +  +++L PLAPLH
Sbjct: 50  AAMQVVFDSLASDGHRLDDLGLVAVGHRVVHGGQDLYRPTVVDDATIARLKELSPLAPLH 109

Query: 125 NPANVDGIDVARKILPDVPHVAVFDTGFFHSLPPAAALYAINKDVAAEHGIRRYGFHGTS 184
           NP  + GI+VARK LPD+PHVAVFDT FFH LPPAAA YAI+ +VA    IRRYGFHGTS
Sbjct: 110 NPPAILGIEVARKALPDLPHVAVFDTAFFHDLPPAAATYAIDAEVAGSWHIRRYGFHGTS 169

Query: 185 HEFVSKRVVEILEKPTEDINTITFHLGNGASMAAVQGGRAVDTSMGMTPLAGLVMGTRSG 244
           H++VS++    L  P E ++ I  HLGNGAS +A+ GGR V+TSMG+TP+ GLVMGTRSG
Sbjct: 170 HQYVSEQAAAFLNVPLESLSQIVLHLGNGASASAILGGRPVETSMGLTPMEGLVMGTRSG 229

Query: 245 DIDPGIVFHLSRTAGMSIDEIDNLLNKKSGVKGLSGVNDFRELREMIDNNDQDAWSAYNI 304
           D+DPG++F+L RTAGMS+++I+ +LN++SGV+GL G  DFR L + I++ D  A  AY++
Sbjct: 230 DVDPGVIFYLWRTAGMSVEDIEAMLNRRSGVRGLGGEIDFRVLHQRIESGDAAAQLAYDV 289

Query: 305 YIHQLRRYLGSYMVALGRVDTIVFTAGVGENAQFVREDALAGLEMYGIEIDPERNALPND 364
           YIH+LR+Y+G+Y+  LG VD I FTAGVGEN   VR D L+GL  +GIE+D   NA P  
Sbjct: 290 YIHRLRKYVGAYLATLGSVDVITFTAGVGENDAAVRRDVLSGLTAFGIELDEHLNASPAR 349

Query: 365 GPRLISTDASKVKVFVIPTNEELAIAR 391
             R IS D + + V V+PTNEELAIAR
Sbjct: 350 TARRISPDGAPITVLVVPTNEELAIAR 376


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: 494
Number of extensions: 14
Number of successful extensions: 2
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: 389
Length adjustment: 31
Effective length of query: 366
Effective length of database: 358
Effective search space:   131028
Effective search space used:   131028
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_011777976.1 MVAN_RS03540 (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.10686.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.8e-124  400.1   0.0   1.2e-123  398.7   0.0    1.5  1  lcl|NCBI__GCF_000015305.1:WP_011777976.1  MVAN_RS03540 acetate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015305.1:WP_011777976.1  MVAN_RS03540 acetate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  398.7   0.0  1.2e-123  1.2e-123       3     401 ..       2     379 ..       1     382 [. 0.95

  Alignments for each domain:
  == domain 1  score: 398.7 bits;  conditional E-value: 1.2e-123
                                 TIGR00016   3 skkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkl 71 
                                               s+ +lvln+Gsss+k+a+l+   s  ++++g+veri  e+a              + a++dh++a++ +
  lcl|NCBI__GCF_000015305.1:WP_011777976.1   2 SRSVLVLNSGSSSVKYAVLEPD-SGVLVADGIVERIGEEGA--------------ERAVTDHAAAMQVV 55 
                                               5689****************99.57777*******998877..............457899******** PP

                                 TIGR00016  72 lntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlkl 140
                                               +++l +d + + +   + ++GHRvvhGg+++   ++v+d +++++k++s+lAPlHnp+++ gie +   
  lcl|NCBI__GCF_000015305.1:WP_011777976.1  56 FDSLASDGH-RLDDLGLVAVGHRVVHGGQDLYRPTVVDDATIARLKELSPLAPLHNPPAILGIEVAR-- 121
                                               *****7554.4444467789**********************************************9.. PP

                                 TIGR00016 141 kvllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnl 209
                                               k l++ ++vavFDtaf + +p  a+ Ya+  ++     +RrYGfHGtsh+yv+++aa  ln pl++l  
  lcl|NCBI__GCF_000015305.1:WP_011777976.1 122 KALPDLPHVAVFDTAFFHDLPPAAATYAIDAEVAGSWHIRRYGFHGTSHQYVSEQAAAFLNVPLESLSQ 190
                                               8899999************************************************************** PP

                                 TIGR00016 210 ivcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksG 278
                                               iv+HlGnGas sa+  G+ ++tsmGltP+eGlvmGtRsGd+Dp++i+yl  t g+s+++ie +ln++sG
  lcl|NCBI__GCF_000015305.1:WP_011777976.1 191 IVLHLGNGASASAILGGRPVETSMGLTPMEGLVMGTRSGDVDPGVIFYLWRTAGMSVEDIEAMLNRRSG 259
                                               ********************************************************************* PP

                                 TIGR00016 279 llgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevre 347
                                               + g+ g   D+R++ +++e g+  a+lA++vy+hR++ky+g+y+a+l g++D i Ft+G+Gen+a vr+
  lcl|NCBI__GCF_000015305.1:WP_011777976.1 260 VRGLGG-EIDFRVLHQRIESGDAAAQLAYDVYIHRLRKYVGAYLATL-GSVDVITFTAGVGENDAAVRR 326
                                               ******.99**************************************.55******************* PP

                                 TIGR00016 348 lvleklevlGlkldlelnnaarsgkesvisteeskvkvlviptneelviaeDal 401
                                               +vl++l  +G++ld++ln  +   + + is + + ++vlv+ptneel+ia+ ++
  lcl|NCBI__GCF_000015305.1:WP_011777976.1 327 DVLSGLTAFGIELDEHLNA-SPARTARRISPDGAPITVLVVPTNEELAIARACA 379
                                               ******************9.88888999**********************9775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (389 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: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 4.04
//
[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