Alignments for a candidate for ackA in Marivita geojedonensis DPG-138

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Marivita geojedonensis DPG-138

Align Acetate kinase; Acetokinase; EC 2.7.2.1 (characterized)
to candidate WP_085635099.1 MGEO_RS02500 acetate/propionate family kinase

Query= SwissProt::P37877
         (395 letters)



>NCBI__GCF_002115805.1:WP_085635099.1
          Length = 386

 Score =  266 bits (680), Expect = 7e-76
 Identities = 161/390 (41%), Positives = 234/390 (60%), Gaps = 17/390 (4%)

Query: 4   IIAINAGSSSLKFQLFEMPSETVLTKGLVERIGIADSVFTISVNGEKNTEVTDIPDHAVA 63
           I+ +NAGSSS+KF LF+     +L+ G+ E IG A     + +  EK+  V  + DH  A
Sbjct: 10  ILVLNAGSSSIKFALFDDALNEILS-GMAEAIGGAS---ILRIGDEKHDVV--LIDHRAA 63

Query: 64  VKMLLNKLTEFGIIKDLNEIDGIGHRVVHGGEKFSDSVLLTDETIKEIEDISELAPLHNP 123
           ++ +L  L+E GI  D   +  +GHRVVHGG K +  + +TDE   EI + + LAPLHNP
Sbjct: 64  LEAILKALSERGITPDT--LRAVGHRVVHGGRKLTAPMRVTDEVRAEIANCTPLAPLHNP 121

Query: 124 ANIVGIKAFKEVLPNVPAVAVFDTAFHQTMPEQSYLYSLPYEYYEKFGIRKYGFHGTSHK 183
            N+  ++A   + P++P  A FDT+FH T P  +  Y++P +  E  GIR+YGFHG S+ 
Sbjct: 122 HNLAPMEALSRLAPDLPQFASFDTSFHATNPNVATRYAIP-KMMETKGIRRYGFHGLSYA 180

Query: 184 YVTERAAELLGRPLKDLRLISCHLGNGASIAAVEGGKSIDTSMGFTPLAGVAMGTRSGNI 243
            +  R  E+ G  L   RL++ HLGNGAS+ A+  G+SI T+MG++PL G+ MGTRSG I
Sbjct: 181 SLVRRLPEISGEALPS-RLLAFHLGNGASLCAIHNGQSIATTMGYSPLDGLTMGTRSGGI 239

Query: 244 DPALIPYIMEKTGQTADEVLNTLNKKSGLLGISGFSSDLRDIVEATKEGNERAETALEVF 303
           D   +  ++ + G    + +  LN +SGLLG+SG  SD+R ++    + +  +  A+E F
Sbjct: 240 DANAVLRLVGENGLERTKAI--LNHESGLLGLSGGKSDMRKLM---LDASAESAFAVEHF 294

Query: 304 ASRIHKYIGSYAARMSGVDAIIFTAGIGENSVEVRERVLRGLEFMGVYWDPALNNVRGEE 363
                ++ GS  A + G+DAI FT GIGEN+V VR R+LRGLE+ GV  +P  N+  G  
Sbjct: 295 CYWTLRHAGSLIAALEGLDAIAFTGGIGENAVGVRARILRGLEWAGVRINPDFNHRSGPR 354

Query: 364 AFISYPHSPVKVMIIPTDEEVMIARDVVRL 393
             +    S V V +IP +EE MIA D   L
Sbjct: 355 --LHAESSKVAVWVIPAEEERMIAMDAQAL 382


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: 386
Number of extensions: 21
Number of successful extensions: 8
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: 386
Length adjustment: 31
Effective length of query: 364
Effective length of database: 355
Effective search space:   129220
Effective search space used:   129220
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_085635099.1 MGEO_RS02500 (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.1827316.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.1e-106  340.2   0.0   8.5e-106  340.0   0.0    1.0  1  NCBI__GCF_002115805.1:WP_085635099.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002115805.1:WP_085635099.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  340.0   0.0  8.5e-106  8.5e-106       6     403 ..      10     382 ..       6     384 .. 0.91

  Alignments for each domain:
  == domain 1  score: 340.0 bits;  conditional E-value: 8.5e-106
                             TIGR00016   6 ilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkkd 78 
                                           ilvlnaGsss+kfal+d +  ++ +lsg++e+i  +      +  g++k  + +   dh++a++++l++l  +
  NCBI__GCF_002115805.1:WP_085635099.1  10 ILVLNAGSSSIKFALFDDAL-NE-ILSGMAEAIGGASI----LRIGDEK--HDVVLIDHRAALEAILKALS-E 73 
                                           9****************993.44.59******987766....4456444..4556789*************.5 PP

                             TIGR00016  79 kkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknvav 151
                                           + i+   + ++++GHRvvhGg k+t  + vtdev ++i++ ++lAPlHnp +l  +ea++     ++ ++ a 
  NCBI__GCF_002115805.1:WP_085635099.1  74 RGIT--PDTLRAVGHRVVHGGRKLTAPMRVTDEVRAEIANCTPLAPLHNPHNLAPMEALS--RLAPDLPQFAS 142
                                           7775..5789**************************************************..7788899**** PP

                             TIGR00016 152 FDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsavk 224
                                           FDt+fH t p+ a  Ya+P ++++ +g+RrYGfHG+s+  + +r+ ++ +  +  ++l+  HlGnGas++a++
  NCBI__GCF_002115805.1:WP_085635099.1 143 FDTSFHATNPNVATRYAIP-KMMETKGIRRYGFHGLSYASLVRRLPEISGE-ALPSRLLAFHLGNGASLCAIH 213
                                           *******************.889999***********************99.56789**************** PP

                             TIGR00016 225 nGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkke 297
                                           nG+si t+mG  PL+Gl mGtRsG iD  ++  l  ++g  l+  + +ln +sGllg+sg  sD+R+++ +  
  NCBI__GCF_002115805.1:WP_085635099.1 214 NGQSIATTMGYSPLDGLTMGTRSGGIDANAVLRLVGENG--LERTKAILNHESGLLGLSGGKSDMRKLMLDA- 283
                                           ***************************998888877666..5677899*******************98777. PP

                             TIGR00016 298 egneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaars 370
                                               e++ A++ +++   ++ g+ ia+leg lDai FtgGiGena+ vr+++l++le  G++++++ n+  rs
  NCBI__GCF_002115805.1:WP_085635099.1 284 --SAESAFAVEHFCYWTLRHAGSLIAALEG-LDAIAFTGGIGENAVGVRARILRGLEWAGVRINPDFNH--RS 351
                                           ..44679*********************99.*************************************9..44 PP

                             TIGR00016 371 gkesvisteeskvkvlviptneelviaeDalrl 403
                                           g    +  e skv v vip +ee +ia Da  l
  NCBI__GCF_002115805.1:WP_085635099.1 352 G--PRLHAESSKVAVWVIPAEEERMIAMDAQAL 382
                                           3..4466789*******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (386 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 31.22
//
[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 2024 update 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