GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Thermithiobacillus tepidarius DSM 3134

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_038019545.1 G579_RS17140 acetate/propionate family kinase

Query= BRENDA::G4T0C7
         (401 letters)



>NCBI__GCF_000423825.1:WP_038019545.1
          Length = 381

 Score =  282 bits (721), Expect = 1e-80
 Identities = 168/394 (42%), Positives = 222/394 (56%), Gaps = 27/394 (6%)

Query: 7   NILVINSGSSSIKYRLIALPQEQVLADGLLERIGEQESRIIHRADDSGRLNEIKQSVIAA 66
           +ILVIN+GSSS+K  L      Q L     +RIG     I+ +   SG     +Q  + +
Sbjct: 2   HILVINAGSSSLKAELWDSSSAQALLRWHAQRIGSAHGAIVSQ---SGSAPARRQVQMLS 58

Query: 67  DHHQAFKAVFEILGENCSVDAIGHRVVHGGDRFSGPALVDDDTIASMRALCRIAPLHNPV 126
            H  AF+A+   LG   +   +GHRVVHGG  +     +DD   A +R L  ++PLH P+
Sbjct: 59  SHADAFQALLRELGGQPAFQRVGHRVVHGGPDYVRSTWLDDRVCAELRRLVPLSPLHQPL 118

Query: 127 NLLGIESCLAHFPGVPQVAVFDTAFHQTMPPHAYRYAIPETWYSDYGIRRFGFHGTS--- 183
           NL  I++    +P +PQ AVFDT FH T+PP A  YA+P+TW  D+G+RR+GFHG +   
Sbjct: 119 NLQLIDASRQAWPAIPQAAVFDTEFHATLPPVAREYALPQTW-RDWGVRRYGFHGIACED 177

Query: 184 --HHYVARRAAEFIGKPFDRSHLITLHLGNGASATAIANGRSVDTSMGFTPLEGLVMGTR 241
             H   A RA          S L+  HLG+GAS TA+ +G SVDTSMG TPLEGLVM TR
Sbjct: 178 VLHQLGAARA----------SRLVICHLGSGASVTAVRDGASVDTSMGMTPLEGLVMATR 227

Query: 242 SGDLDPAIPLFVEQTENTDTDAIDRALNRESGLKGLCGTNDLRTVLEQTNAGDERARLAL 301
           SGD+DP   L++ +        +DR LN  SGL GL G  D+  +L    A    AR A+
Sbjct: 228 SGDVDPGALLYLLRERGVSPAELDRGLNEASGLLGLAGDRDMAHLLA---ADTPAARFAV 284

Query: 302 DLYCYRIKKYIGAYYAVLGEVDALVFTGGVGENAAEVRRLACEGLSRLGIAIDEAANSDV 361
           +L+CYR++K IGAY A LG +D LVF+GG+GENA  VR   C  L  LG+ +D AAN   
Sbjct: 285 ELFCYRVRKAIGAYAAALGGLDQLVFSGGIGENAPAVRAAICAPLDFLGVRLDPAAN--- 341

Query: 362 TGAIAEIGLAESRTRILVIKTDEELQIAREAMAV 395
             A  E  LA     +  I  +E   I R   A+
Sbjct: 342 --AANEARLATGPVDVHRIAVNENRAITRAVAAL 373


Lambda     K      H
   0.320    0.137    0.400 

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: 450
Number of extensions: 17
Number of successful extensions: 5
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: 401
Length of database: 381
Length adjustment: 31
Effective length of query: 370
Effective length of database: 350
Effective search space:   129500
Effective search space used:   129500
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 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate WP_038019545.1 G579_RS17140 (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.2598057.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     5e-102  327.6   0.0   6.2e-102  327.3   0.0    1.0  1  NCBI__GCF_000423825.1:WP_038019545.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000423825.1:WP_038019545.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  327.3   0.0  6.2e-102  6.2e-102       4     400 ..       1     370 [.       1     374 [. 0.92

  Alignments for each domain:
  == domain 1  score: 327.3 bits;  conditional E-value: 6.2e-102
                             TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 
                                           + ilv+naGssslk  l+d + s + ll+  ++ri +++  i   + +   +++++  ++h+ a ++ll++l 
  NCBI__GCF_000423825.1:WP_038019545.1   1 MHILVINAGSSSLKAELWDSS-SAQALLRWHAQRIGSAHGAIVSQSGSAPARRQVQMLSSHADAFQALLRELG 72 
                                           579******************.678889**********998887777778888889999*************9 PP

                             TIGR00016  77 kdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknv 149
                                                   +   + +GHRvvhGg ++  s+ ++d v ++++++++l PlH p +l+ i+a    +  +  ++ 
  NCBI__GCF_000423825.1:WP_038019545.1  73 G-------QPAFQRVGHRVVHGGPDYVRSTWLDDRVCAELRRLVPLSPLHQPLNLQLIDASR--QAWPAIPQA 136
                                           5.......567899**********************************************99..7788899** PP

                             TIGR00016 150 avFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsa 222
                                           avFDt fH t+p  a +YalP + +++ gvRrYGfHG++ +     + + l+  +  ++l++cHlG Gasv+a
  NCBI__GCF_000423825.1:WP_038019545.1 137 AVFDTEFHATLPPVAREYALP-QTWRDWGVRRYGFHGIACE----DVLHQLGA-ARASRLVICHLGSGASVTA 203
                                           *********************.8899***********9864....45556776.6889*************** PP

                             TIGR00016 223 vknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildk 295
                                           v++G s+dtsmG+tPLeGlvm tRsGd+Dp+++ yl  ++g s +e+ + ln  sGllg++g   D+ ++l++
  NCBI__GCF_000423825.1:WP_038019545.1 204 VRDGASVDTSMGMTPLEGLVMATRSGDVDPGALLYLLRERGVSPAELDRGLNEASGLLGLAG-DRDMAHLLAA 275
                                           **************************************************************.7788887776 PP

                             TIGR00016 296 keegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaa 368
                                                  a+ A++++++R++k ig+y+a+l g lD +vF gGiGena  vr+ ++  l++lG++ld++ n   
  NCBI__GCF_000423825.1:WP_038019545.1 276 D---TPAARFAVELFCYRVRKAIGAYAAALGG-LDQLVFSGGIGENAPAVRAAICAPLDFLGVRLDPAANA-- 342
                                           6...7789**********************76.***********************************999.. PP

                             TIGR00016 369 rsgkesvisteeskvkvlviptneelviaeDa 400
                                              +e+ ++   + v v +i  ne+ +i + +
  NCBI__GCF_000423825.1:WP_038019545.1 343 --ANEARLA--TGPVDVHRIAVNENRAITRAV 370
                                           ..4444444..588899999999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (381 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: 14.56
//
[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