Alignments for a candidate for ackA in Magnetospirillum magneticum AMB-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Magnetospirillum magneticum AMB-1

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_011384935.1 AMB_RS12860 acetate/propionate family kinase

Query= BRENDA::Q9WYB1
         (403 letters)



>NCBI__GCF_000009985.1:WP_011384935.1
          Length = 397

 Score =  290 bits (741), Expect = 7e-83
 Identities = 161/409 (39%), Positives = 265/409 (64%), Gaps = 28/409 (6%)

Query: 3   VLVINSGSSSIKYQLIEMEGEK---VLCKGIAERIGIEGSRLVHRVGDEKH---VIEREL 56
           +LVIN+GSSSIK+ L    G++   + CKG  E I +      H +    H   + E+  
Sbjct: 5   ILVINAGSSSIKFSLYISNGDEKPLLSCKGQVEGINVAP----HFIAKSPHGGVLNEQRW 60

Query: 57  PDH----EEALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAI 112
           PD      EAL   +   ++ +LG      E+ A GHRVVHGG ++ + +LV++E+++ +
Sbjct: 61  PDQPNMSHEALFKYMIEWIEAQLGDA----ELKAAGHRVVHGGSQYSQPLLVNDELMEEL 116

Query: 113 EEVSPLAPLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYK 172
           E++ PLAPLH P NL  I+A  K+ PG+  VA FDTAFH++ P  A  +A+P +   +  
Sbjct: 117 EKLIPLAPLHQPHNLAPIRALTKVHPGLTQVACFDTAFHRSNPWTAQSFALPRKITGE-G 175

Query: 173 IRRYGFHGTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPL 232
           ++RYGFHG S+ +++++  + L       K++ CH+G+GAS+ A+  GK V ++MGFT +
Sbjct: 176 VKRYGFHGLSYEFIARQMRQ-LSPAAARGKVVVCHLGSGASMCAIDGGKSVASTMGFTAV 234

Query: 233 EGLVMGTRSGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAAL 292
           +GL MGTR+G +D  +  ++++++G++P+E+ D+L K+SG+ G+S G S+DMR + E++ 
Sbjct: 235 DGLPMGTRTGTMDAGVILYLLQQKGMTPKEIEDLLYKQSGLLGVS-GVSNDMRILLESS- 292

Query: 293 KGDEWCKLVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGV 352
             +      +E++ YRI++ +G+ AAAM G+DA+VFTAG+GE SP  RE VC++ E+LGV
Sbjct: 293 --EPHAAEAVELFVYRISRELGSLAAAMGGLDALVFTAGIGERSPQIRERVCAHAEWLGV 350

Query: 353 KLDKQKNEETIRGKEGIISTPDSRVKVLVVPTNEELMIARDTKEIVEKI 401
           ++D++ N+        +IS  DS V V V+PT+EE+MIA+ T+E++  +
Sbjct: 351 EMDQEANQR----DSLLISAADSPVSVWVIPTDEEMMIAKHTRELLRSL 395


Lambda     K      H
   0.318    0.138    0.391 

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: 423
Number of extensions: 27
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: 403
Length of database: 397
Length adjustment: 31
Effective length of query: 372
Effective length of database: 366
Effective search space:   136152
Effective search space used:   136152
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_011384935.1 AMB_RS12860 (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.26632.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-116  375.6   0.0   1.5e-116  375.4   0.0    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011384935.1  AMB_RS12860 acetate/propionate f


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011384935.1  AMB_RS12860 acetate/propionate family kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  375.4   0.0  1.5e-116  1.5e-116       5     403 ..       4     391 ..       1     393 [. 0.90

  Alignments for each domain:
  == domain 1  score: 375.4 bits;  conditional E-value: 1.5e-116
                                 TIGR00016   5 kilvlnaGssslkfalldaensekvl..lsglverikleeariktvedgekkeeek...laiedheeav 68 
                                                ilv+naGsss+kf+l+  ++ ek l  ++g ve i+++  +i +  +g+  +e+    +   +he+  
  lcl|NCBI__GCF_000009985.1:WP_011384935.1   4 GILVINAGSSSIKFSLYISNGDEKPLlsCKGQVEGINVAPHFIAKSPHGGVLNEQRwpdQPNMSHEALF 72 
                                               69***************99987777622589**********9999977765444431113334555666 PP

                                 TIGR00016  69 kkllntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieav 137
                                               k +++ +++    +   +e+++ GHRvvhGg+++++  +v+de +++++++++lAPlH p +l  i+a+
  lcl|NCBI__GCF_000009985.1:WP_011384935.1  73 KYMIEWIEA----QLGDAELKAAGHRVVHGGSQYSQPLLVNDELMEELEKLIPLAPLHQPHNLAPIRAL 137
                                               778888886....55789*************************************************** PP

                                 TIGR00016 138 lklkvllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkpldd 206
                                               +  kv++   +va+FDtafH+  p  a  +alP+++ +  gv+rYGfHG+s++++++++ + l  +++ 
  lcl|NCBI__GCF_000009985.1:WP_011384935.1 138 T--KVHPGLTQVACFDTAFHRSNPWTAQSFALPRKI-TGEGVKRYGFHGLSYEFIARQMRQ-LSPAAAR 202
                                               *..6677777***********************766.667****************99865.6777999 PP

                                 TIGR00016 207 lnlivcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnk 275
                                                +++vcHlG Gas++a+  Gks+  +mG+t ++Gl mGtR+G +D ++i yl +++g++ +eie++l k
  lcl|NCBI__GCF_000009985.1:WP_011384935.1 203 GKVVVCHLGSGASMCAIDGGKSVASTMGFTAVDGLPMGTRTGTMDAGVILYLLQQKGMTPKEIEDLLYK 271
                                               ********************************************************************* PP

                                 TIGR00016 276 ksGllgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaae 344
                                               +sGllg+sg+s+D+R +l+     + +a+ A++++v+Ri + +g+ +a++ g lDa+vFt+GiGe + +
  lcl|NCBI__GCF_000009985.1:WP_011384935.1 272 QSGLLGVSGVSNDMRILLESS---EPHAAEAVELFVYRISRELGSLAAAMGG-LDALVFTAGIGERSPQ 336
                                               *****************9998...5669**********************76.**************** PP

                                 TIGR00016 345 vrelvleklevlGlkldlelnnaarsgkesvisteeskvkvlviptneelviaeDalrl 403
                                               +re+v+ + e lG+++d+e n+     ++ +is  +s v v vipt+ee++ia+ + +l
  lcl|NCBI__GCF_000009985.1:WP_011384935.1 337 IRERVCAHAEWLGVEMDQEANQ----RDSLLISAADSPVSVWVIPTDEEMMIAKHTREL 391
                                               ********************99....8999***********************987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (397 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.02
//
[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