GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Rhodobacter ovatus JA234

Align Acetate kinase; Acetokinase; EC 2.7.2.1 (characterized)
to candidate WP_097031061.1 CRO07_RS12690 acetate/propionate family kinase

Query= SwissProt::P37877
         (395 letters)



>NCBI__GCF_900207575.1:WP_097031061.1
          Length = 396

 Score =  257 bits (656), Expect = 5e-73
 Identities = 152/384 (39%), Positives = 228/384 (59%), Gaps = 10/384 (2%)

Query: 5   IAINAGSSSLKFQLFEMPSETVLTKGLVERIGIADSVFTISVNGEKNTEVTDIPDHAVAV 64
           + +N GSS++KF LF++   + L +G VE IG+   +     +G            A  +
Sbjct: 6   LVLNIGSSTVKFGLFDIQDASPLVRGAVEGIGLRPRLKAHLPDGTLELRAPADARDAKEL 65

Query: 65  KMLLNKLTEFGIIKDLNEIDGIGHRVVHGGEKFSDSVLLTDETIKEIEDISELAPLHNPA 124
            + L  L E G +  L ++   GHRVVHGG  F+  VLLT E I+ +E    LAP H P 
Sbjct: 66  TLWLLGLLE-GRLGPL-DLHAAGHRVVHGGPDFNAPVLLTPEVIERLEGFCPLAPGHQPF 123

Query: 125 NIVGIKAFKEVLPNVPAVAVFDTAFHQTMPEQSYLYSLPYEYYEKFGIRKYGFHGTSHKY 184
           N+ GI+A +   P VP VA FDTAFH   P  + LY+LP +  ++ GI +YGFHG S+ +
Sbjct: 124 NLAGIRAVEARWPGVPQVACFDTAFHHDRPRIARLYALPRDLTDQ-GILRYGFHGLSYDF 182

Query: 185 VTERAAELLGRPLKDLRLISCHLGNGASIAAVEGGKSIDTSMGFTPLAGVAMGTRSGNID 244
           V  R  ++LG   +  R+I  HLG+GAS+ A+   KS DT+MGF+ L G+ MGTR G ID
Sbjct: 183 VASRLPDVLGAKARG-RVIVAHLGSGASLCALHDLKSTDTTMGFSALDGLMMGTRCGQID 241

Query: 245 PALIPYIMEKTGQTADEVLNTLNKKSGLLGISGFSSDLRDIVEATKEGNERAETALEVFA 304
           P ++ +++ + G T  E+ + L ++SGLLG+SG S D+RD++++    +  A  A+E+F 
Sbjct: 242 PGVLLHLL-RQGMTGPEIESLLGRQSGLLGVSGLSPDMRDLLDS---DHPEAAEAVELFV 297

Query: 305 SRIHKYIGSYAARMSGVDAIIFTAGIGENSVEVRERVLRGLEFMGVYWDPALNNVRGEEA 364
             + + +G+ AA M G+DA++FTAGIG++S E+R RV+  L ++G+  DP  N       
Sbjct: 298 RFVVRQVGALAAGMGGLDALVFTAGIGQHSPEIRARVMAALGWLGLDPDPEAN--AQSRT 355

Query: 365 FISYPHSPVKVMIIPTDEEVMIAR 388
            +S   S V   +I TDEE +I R
Sbjct: 356 ILSRAGSRVMAAVIATDEEAVILR 379


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: 364
Number of extensions: 22
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: 396
Length adjustment: 31
Effective length of query: 364
Effective length of database: 365
Effective search space:   132860
Effective search space used:   132860
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_097031061.1 CRO07_RS12690 (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.1355907.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.6e-101  325.9   0.0     2e-101  325.6   0.0    1.0  1  NCBI__GCF_900207575.1:WP_097031061.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900207575.1:WP_097031061.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  325.6   0.0    2e-101    2e-101       5     398 ..       4     379 ..       1     384 [. 0.93

  Alignments for each domain:
  == domain 1  score: 325.6 bits;  conditional E-value: 2e-101
                             TIGR00016   5 kilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkk 77 
                                           + lvln Gss +kf l+d ++++ + ++g ve i l       + dg  + ++  + +d +e    ll  l+ 
  NCBI__GCF_900207575.1:WP_097031061.1   4 VWLVLNIGSSTVKFGLFDIQDASPL-VRGAVEGIGLRPRLKAHLPDGTLELRAPADARDAKELTLWLLGLLEG 75 
                                           679*****************86655.************98888888888888888888877766666666664 PP

                             TIGR00016  78 dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknva 150
                                               +    ++++ GHRvvhGg +f+  v++t ev+++++ + +lAP H p +l gi+av      + +++va
  NCBI__GCF_900207575.1:WP_097031061.1  76 ----RLGPLDLHAAGHRVVHGGPDFNAPVLLTPEVIERLEGFCPLAPGHQPFNLAGIRAVE--ARWPGVPQVA 142
                                           ....44566899*************************************************..889999**** PP

                             TIGR00016 151 vFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsav 223
                                           +FDtafH+  p+ a lYalP++l +++g+ rYGfHG+s+ +v+ r+ ++l+   +  ++iv+HlG Gas++a+
  NCBI__GCF_900207575.1:WP_097031061.1 143 CFDTAFHHDRPRIARLYALPRDL-TDQGILRYGFHGLSYDFVASRLPDVLGA-KARGRVIVAHLGSGASLCAL 213
                                           ********************776.678************************9.57789*************** PP

                             TIGR00016 224 knGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkk 296
                                           ++ ks dt+mG+  L+Gl+mGtR+G+iDp+++ +l   +g++  eie++l ++sGllg+sgls D+Rd+ld  
  NCBI__GCF_900207575.1:WP_097031061.1 214 HDLKSTDTTMGFSALDGLMMGTRCGQIDPGVLLHLLR-QGMTGPEIESLLGRQSGLLGVSGLSPDMRDLLDSD 285
                                           **********************************986.79******************************998 PP

                             TIGR00016 297 eegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaar 369
                                              + ea+ A++++v  + + +g+ +a + g lDa+vFt+GiG+ + e+r++v+ +l  lGl+ d+e n    
  NCBI__GCF_900207575.1:WP_097031061.1 286 ---HPEAAEAVELFVRFVVRQVGALAAGMGG-LDALVFTAGIGQHSPEIRARVMAALGWLGLDPDPEANA--- 351
                                           ...78899*********************76.************************************99... PP

                             TIGR00016 370 sgkesvisteeskvkvlviptneelviae 398
                                            ++ +++s   s+v ++vi t+ee vi++
  NCBI__GCF_900207575.1:WP_097031061.1 352 -QSRTILSRAGSRVMAAVIATDEEAVILR 379
                                           .778999********************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (396 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: 14.73
//
[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:

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