GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Methylocapsa aurea KYG

Align Acetate kinase; Acetokinase; EC 2.7.2.1 (characterized)
to candidate WP_036261519.1 DL86_RS11535 acetate/propionate family kinase

Query= SwissProt::P37877
         (395 letters)



>NCBI__GCF_000746085.1:WP_036261519.1
          Length = 400

 Score =  286 bits (733), Expect = 6e-82
 Identities = 166/398 (41%), Positives = 244/398 (61%), Gaps = 23/398 (5%)

Query: 4   IIAINAGSSSLKFQLFEMPSE--TVLTKGLVERIGIADSVFTISVNG-----EKNTEVTD 56
           ++ +NAGSSS+KF LFE+       L  GLVE +G    +      G     +  T+  D
Sbjct: 5   VVTLNAGSSSIKFALFELNGREPVALAVGLVEMLGEQRRLKARDGGGAPIHEDAWTDAGD 64

Query: 57  IPDHAVAVKMLLNKLTEFGIIKDLNEIDGIGHRVVHGGEKFSDSVLLTDETIKEIEDISE 116
            P H  A++ +L      G   + N +   GHRVVHGG  F    L+TDE ++ +E +S 
Sbjct: 65  APFHTEALRRVL--AWRLGAFPEANVV-AAGHRVVHGGVYFDAPALVTDEVLRILESLSP 121

Query: 117 LAPLHNPANIVGIKAFKEVLPNVPAVAVFDTAFHQTMPEQSYLYSLPYEYYEKFGIRKYG 176
           LAPLH P NI GI A +E  P+V  VA FDTAFH+  P  + +++LP ++Y++ G+R+YG
Sbjct: 122 LAPLHQPHNIAGILAAREAWPHVRQVACFDTAFHRAHPFVNDVFALPRKFYDE-GVRRYG 180

Query: 177 FHGTSHKYVTERAAELLGRPLKDL-RLISCHLGNGASIAAVEGGKSIDTSMGFTPLAGVA 235
           FHG S++YVTE+  ++   PL    R++  HLGNGAS+ A+  G S+ +SMGFT L G+ 
Sbjct: 181 FHGLSYEYVTEKLQQV--APLHAAGRVVVAHLGNGASMCAIRDGLSVASSMGFTALDGLP 238

Query: 236 MGTRSGNIDPALIPYIMEKTGQTADEVLNTLNKKSGLLGISGFSSDLRDIVEATKEGNER 295
           MGTR G +DP ++ Y+M++   +A+ + + L ++SGL G+SG S D+R++     E ++R
Sbjct: 239 MGTRCGQLDPGVVLYLMQEMKMSAEAIADLLYRESGLKGLSGVSHDMREL-----EASDR 293

Query: 296 AET--ALEVFASRIHKYIGSYAARMSGVDAIIFTAGIGENSVEVRERVLRGLEFMGVYWD 353
            E   A+E F  RI + +G  AA + G+DA++F  GIGE++  VRERVL G+E++G+  D
Sbjct: 294 PEARQAIEYFVFRIRRELGGLAAVLEGLDAMVFCGGIGEHAWRVRERVLEGMEWIGIELD 353

Query: 354 PALNNVRGEEAFISYPHSPVKVMIIPTDEEVMIARDVV 391
              N  R  E  IS   S V+V +IPTDEE MIAR  +
Sbjct: 354 RTAN--RASEQVISSQRSRVRVFVIPTDEEAMIARQTL 389


Lambda     K      H
   0.317    0.136    0.381 

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: 340
Number of extensions: 12
Number of successful extensions: 6
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: 395
Length of database: 400
Length adjustment: 31
Effective length of query: 364
Effective length of database: 369
Effective search space:   134316
Effective search space used:   134316
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_036261519.1 DL86_RS11535 (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.662794.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-114  369.3   0.0   1.2e-114  369.1   0.0    1.0  1  NCBI__GCF_000746085.1:WP_036261519.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000746085.1:WP_036261519.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  369.1   0.0  1.2e-114  1.2e-114       4     402 ..       3     390 ..       1     393 [. 0.90

  Alignments for each domain:
  == domain 1  score: 369.1 bits;  conditional E-value: 1.2e-114
                             TIGR00016   4 kkilvlnaGssslkfalldaensekv.llsglverikleeariktvedg.....ekkeeeklaiedheeavkk 70 
                                           + ++ lnaGsss+kfal++ ++ e v l+ glve++  +   +k    g     e+  ++  + + h+ea+++
  NCBI__GCF_000746085.1:WP_036261519.1   3 RHVVTLNAGSSSIKFALFELNGREPVaLAVGLVEMLGEQRR-LKARDGGgapihEDAWTDAGDAPFHTEALRR 74 
                                           67999****************988777999****9987766.4444333111112333445556668888888 PP

                             TIGR00016  71 llntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvl 143
                                           +l            ++++ + GHRvvhGg +f   ++vtdevl+ ++ +s+lAPlH p ++ gi a+   +  
  NCBI__GCF_000746085.1:WP_036261519.1  75 VLAWRLG----AFPEANVVAAGHRVVHGGVYFDAPALVTDEVLRILESLSPLAPLHQPHNIAGILAAR--EAW 141
                                           7765553....3466789999**********************************************9..888 PP

                             TIGR00016 144 lkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGn 216
                                           +++++va+FDtafH+  p  + ++alP+++y+e gvRrYGfHG+s++yvt++++++     +  +++v+HlGn
  NCBI__GCF_000746085.1:WP_036261519.1 142 PHVRQVACFDTAFHRAHPFVNDVFALPRKFYDE-GVRRYGFHGLSYEYVTEKLQQVAPL-HAAGRVVVAHLGN 212
                                           9999***********************999976.9******************999887.67889******** PP

                             TIGR00016 217 GasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDl 289
                                           Gas++a+++G s+  smG+t L+Gl mGtR+G++Dp+++ yl+++ ++s+++i ++l ++sGl g+sg+s D+
  NCBI__GCF_000746085.1:WP_036261519.1 213 GASMCAIRDGLSVASSMGFTALDGLPMGTRCGQLDPGVVLYLMQEMKMSAEAIADLLYRESGLKGLSGVSHDM 285
                                           ************************************************************************* PP

                             TIGR00016 290 RdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldl 362
                                           R++++     + ea+ A++ +v Ri++ +g  +a leg lDa+vF gGiGe a  vre+vle++e +G++ld 
  NCBI__GCF_000746085.1:WP_036261519.1 286 RELEASD---RPEARQAIEYFVFRIRRELGGLAAVLEG-LDAMVFCGGIGEHAWRVRERVLEGMEWIGIELDR 354
                                           **99877...7789**********************99.*********************************9 PP

                             TIGR00016 363 elnnaarsgkesvisteeskvkvlviptneelviaeDalr 402
                                             n      +e+vis++ s+v+v+vipt+ee +ia+ +l 
  NCBI__GCF_000746085.1:WP_036261519.1 355 TANR----ASEQVISSQRSRVRVFVIPTDEEAMIARQTLA 390
                                           9988....7899***********************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (400 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 28.43
//
[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:

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:

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:

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:

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