Alignments for a candidate for ackA in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Dyella japonica UNC79MFTsu3.2

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate N515DRAFT_2456 N515DRAFT_2456 acetate kinase

Query= BRENDA::G4T0C7
         (401 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2456
          Length = 401

 Score =  258 bits (658), Expect = 3e-73
 Identities = 162/398 (40%), Positives = 223/398 (56%), Gaps = 15/398 (3%)

Query: 5   NGNILVINSGSSSIKYRLIA--LPQEQVLADGLLERIGEQESRIIHRADDSGRLNEIKQS 62
           NG IL +N+GSSSIK+ L    L  ++++  G +E IG  E R      D   ++    +
Sbjct: 2   NGIILALNAGSSSIKFALHEHRLAAQRLILRGAIEGIGA-EPRFTAWQPDGAIIDREAWA 60

Query: 63  VIAADHHQAFKAVFEILGEN---CSVDAIGHRVVHGGDRFSGPALVDDDTIASMRALCRI 119
             AA H Q  + +   +        +  +GHRVVHGG  F  P  +D   +  +  L  +
Sbjct: 61  DAAAPHEQLLQPLLAWITARLGAAELAVVGHRVVHGGPSFGQPVRIDTPVMQELERLVSL 120

Query: 120 APLHNPVNLLGIESCLAHFPGVPQVAVFDTAFHQTMPPHAYRYAIPETWYSDYGIRRFGF 179
           APLH P  L    +     PG+ QVA FDTAFH+ MP  A    +P   Y+D G+RR+GF
Sbjct: 121 APLHQPHPLAAARAIARLRPGLMQVACFDTAFHRGMPAVAASLGLPRA-YADDGMRRYGF 179

Query: 180 HGTSHHYVARRAAEFIGKPFDRSHLITLHLGNGASATAIANGRSVDTSMGFTPLEGLVMG 239
           HG S+ Y+A R  EF  +  D   +I  HLGNGAS  A+ +GRS+DT+MGF+ L+GLVMG
Sbjct: 180 HGLSYEYLAGRLREFAPELAD-GRVIMAHLGNGASLCAMRHGRSIDTTMGFSALDGLVMG 238

Query: 240 TRSGDLDPAIPLFVEQTENTDTDAIDRALNRESGLKGLCGTN-DLRTVLEQTNAGDERAR 298
           +R G LDP   L + Q       AI+  L +ESGL G+ G + D+R +L   +     AR
Sbjct: 239 SRCGSLDPGAVLHLLQARGLSVAAIEHLLYQESGLLGVSGISADMRALLASDSG---HAR 295

Query: 299 LALDLYCYRIKKYIGAYYAVLGEVDALVFTGGVGENAAEVRRLACEGLSRLGIAIDEAAN 358
            A++L+ YRI K IGA  +V G +DALVF+ G+GE+AA +R   C  L+ LG+  DE+AN
Sbjct: 296 EAIELFVYRIVKEIGALTSVAGGLDALVFSAGIGEHAASIRSAVCRALAWLGVECDESAN 355

Query: 359 SDVTGAIAEIGLAESRTRILVIKTDEELQIAREAMAVL 396
                 I+    A S  R+ VI+TDEE  IA  A  VL
Sbjct: 356 GLHKMLIS---TAHSAVRVFVIRTDEEAVIAAHAAGVL 390


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: 417
Number of extensions: 18
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: 401
Length of database: 401
Length adjustment: 31
Effective length of query: 370
Effective length of database: 370
Effective search space:   136900
Effective search space used:   136900
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 N515DRAFT_2456 N515DRAFT_2456 (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.4909.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   2.2e-111  358.4   0.0   2.5e-111  358.2   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_2456  N515DRAFT_2456 acetate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_2456  N515DRAFT_2456 acetate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  358.2   0.0  2.5e-111  2.5e-111       5     400 ..       4     386 ..       1     391 [. 0.92

  Alignments for each domain:
  == domain 1  score: 358.2 bits;  conditional E-value: 2.5e-111
                                    TIGR00016   5 kilvlnaGssslkfalldaen.sekvllsglverikleeariktvedge..kkeeeklaiedheea 67 
                                                   il lnaGsss+kfal +++  +++++l+g +e i  e  +  +  dg   ++e+   a + he+ 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2456   4 IILALNAGSSSIKFALHEHRLaAQRLILRGAIEGIGAEPRFTAWQPDGAiiDREAWADAAAPHEQL 69 
                                                  69****************9873677799************99999888622334444555667777 PP

                                    TIGR00016  68 vkkllntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaeleg 133
                                                  ++ ll  +++    +   +e+a++GHRvvhGg +f + v +++ v+++++++++lAPlH p  l +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2456  70 LQPLLAWITA----RLGAAELAVVGHRVVHGGPSFGQPVRIDTPVMQELERLVSLAPLHQPHPLAA 131
                                                  7777777775....67899*********************************************** PP

                                    TIGR00016 134 ieavlklkvllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakl 199
                                                   +a+ +l + l   +va+FDtafH+ +p  a+  +lP ++y + g+RrYGfHG+s++y++ r+ + 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2456 132 ARAIARLRPGLM--QVACFDTAFHRGMPAVAASLGLP-RAYADDGMRRYGFHGLSYEYLAGRLREF 194
                                                  *****7777666..***********************.88999********************998 PP

                                    TIGR00016 200 lnkplddlnlivcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlgls 265
                                                      l+d ++i++HlGnGas++a++ G+sidt+mG+  L+GlvmG+R+G++Dp+++ +l + +gls
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2456 195 APE-LADGRVIMAHLGNGASLCAMRHGRSIDTTMGFSALDGLVMGSRCGSLDPGAVLHLLQARGLS 259
                                                  766.9************************************************************* PP

                                    TIGR00016 266 ldeieetlnkksGllgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDa 331
                                                  +++ie++l ++sGllg+sg+s+D+R +l+    g+  a+ A++++v+Ri k ig+ ++   g lDa
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2456 260 VAAIEHLLYQESGLLGVSGISADMRALLASD-SGH--AREAIELFVYRIVKEIGALTSVA-GGLDA 321
                                                  ***************************9887.566..9*****************98887.55*** PP

                                    TIGR00016 332 ivFtgGiGenaaevrelvleklevlGlkldlelnnaarsgkesvisteeskvkvlviptneelvia 397
                                                  +vF +GiGe aa++r  v+++l+ lG+++d+  n      ++ +ist +s+v+v+vi+t+ee via
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2456 322 LVFSAGIGEHAASIRSAVCRALAWLGVECDESANG----LHKMLISTAHSAVRVFVIRTDEEAVIA 383
                                                  *******************************9999....8899**********************9 PP

                                    TIGR00016 398 eDa 400
                                                    a
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2456 384 AHA 386
                                                  876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (401 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.45
//
[ok]

This GapMind analysis is from Sep 17 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