Alignments for a candidate for ackA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Klebsiella michiganensis M5al

Align Probable propionate kinase; EC 2.7.2.15 (characterized)
to candidate BWI76_RS23200 BWI76_RS23200 propionate kinase

Query= SwissProt::P74879
         (404 letters)



>FitnessBrowser__Koxy:BWI76_RS23200
          Length = 404

 Score =  703 bits (1814), Expect = 0.0
 Identities = 350/404 (86%), Positives = 377/404 (93%)

Query: 1   MSYKIMAINAGSSSLKFQLLEMPQGDMLCQGLIERIGMADAQVTIKTHSQKWQETVPVAD 60
           MSYKIMAINAGSSSLKFQLLEMPQG+ LCQGLIERIGMA+AQVT+KT +QKWQE+ P+AD
Sbjct: 1   MSYKIMAINAGSSSLKFQLLEMPQGETLCQGLIERIGMANAQVTLKTPAQKWQESAPIAD 60

Query: 61  HRDAVTLLLEKLLGYQIINSLRDIDGVGHRVAHGGEFFKDSTLVTDETLAQIERLAELAP 120
           HR+AVTLLLEKLLGY+II SL+DIDGVGHRVAHGGE FKDST VTDE+LA+IERLAELAP
Sbjct: 61  HREAVTLLLEKLLGYRIIESLQDIDGVGHRVAHGGERFKDSTPVTDESLAEIERLAELAP 120

Query: 121 LHNPVNALGIHVFRQLLPDAPSVAVFDTAFHQTLDEPAYIYPLPWHYYAELGIRRYGFHG 180
           LHNPVNALGI VFRQLLPD PSVAVFDTAFHQTLDE A+IYPLPW YY+ELGIRRYGFHG
Sbjct: 121 LHNPVNALGIKVFRQLLPDTPSVAVFDTAFHQTLDERAFIYPLPWRYYSELGIRRYGFHG 180

Query: 181 TSHKYVSGVLAEKLGVPLSALRVICCHLGNGSSICAIKNGRSVNTSMGFTPQSGVMMGTR 240
           TSHKYVS  LAEKLGVPLSALRV+CCHLGNGSS+CAIK GRSVNTSMGFTPQSGVMMGTR
Sbjct: 181 TSHKYVSATLAEKLGVPLSALRVVCCHLGNGSSVCAIKGGRSVNTSMGFTPQSGVMMGTR 240

Query: 241 SGDIDPSILPWIAQRESKTPQQLNQLLNNESGLLGVSGVSSDYRDVEQAANTGNRQAKLA 300
           SGDIDPSILPW+A  E +TP+QLNQLLNNESGLLGVSGVS DYRDVEQAA+ GNR+A LA
Sbjct: 241 SGDIDPSILPWLALHEGQTPEQLNQLLNNESGLLGVSGVSHDYRDVEQAADGGNRRAALA 300

Query: 301 LTLFAERIRATIGSYIMQMGGLDALVFTGGIGENSARARSAVCHNLQFLGLAVDEEKNQR 360
           L LFAERIRATIGSYIMQMGG+DAL+FTGGIGENSARARSA+CHNL FLGL+VDEEKNQ 
Sbjct: 301 LALFAERIRATIGSYIMQMGGIDALIFTGGIGENSARARSAICHNLNFLGLSVDEEKNQH 360

Query: 361 NATFIQTENALVKVAVINTNEELMIAQDVMRIALPATEGLCVPA 404
           NATFIQ E+ALVKVAVINTNEELMIA+DVMR+ALPA E L V A
Sbjct: 361 NATFIQAEHALVKVAVINTNEELMIARDVMRLALPAAETLTVSA 404


Lambda     K      H
   0.319    0.135    0.392 

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: 630
Number of extensions: 7
Number of successful extensions: 1
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: 404
Length of database: 404
Length adjustment: 31
Effective length of query: 373
Effective length of database: 373
Effective search space:   139129
Effective search space used:   139129
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 BWI76_RS23200 BWI76_RS23200 (propionate 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.9088.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   6.8e-156  505.0   0.0   7.6e-156  504.8   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS23200  BWI76_RS23200 propionate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS23200  BWI76_RS23200 propionate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  504.8   0.0  7.6e-156  7.6e-156       3     404 ..       2     393 ..       1     394 [. 0.97

  Alignments for each domain:
  == domain 1  score: 504.8 bits;  conditional E-value: 7.6e-156
                               TIGR00016   3 skkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkklln 73 
                                             s ki+ +naGssslkf+ll++ ++e++ ++gl+eri +++a+++ +++  +k +e   i+dh+eav+ ll+
  lcl|FitnessBrowser__Koxy:BWI76_RS23200   2 SYKIMAINAGSSSLKFQLLEMPQGETL-CQGLIERIGMANAQVT-LKTPAQKWQESAPIADHREAVTLLLE 70 
                                             579*******************98887.*************776.566668999999************** PP

                               TIGR00016  74 tlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvll 144
                                             +l    +i+++l++i+ +GHRv+hGge+f++s+ vtde+l++i++++elAPlHnp ++ gi+ +   + l+
  lcl|FitnessBrowser__Koxy:BWI76_RS23200  71 KLL-GYRIIESLQDIDGVGHRVAHGGERFKDSTPVTDESLAEIERLAELAPLHNPVNALGIKVFR--QLLP 138
                                             ***.699**********************************************************..7889 PP

                               TIGR00016 145 kaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlG 215
                                             +++ vavFDtafHqt+ e+a++Y+lP+++y elg+RrYGfHGtshkyv+ ++a++l+ pl  l+++ cHlG
  lcl|FitnessBrowser__Koxy:BWI76_RS23200 139 DTPSVAVFDTAFHQTLDERAFIYPLPWRYYSELGIRRYGFHGTSHKYVSATLAEKLGVPLSALRVVCCHLG 209
                                             999******************************************************************** PP

                               TIGR00016 216 nGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisgls 286
                                             nG+sv+a+k G+s++tsmG+tP  G++mGtRsGdiDp+i+ +la ++g++ ++++++ln +sGllg+sg+s
  lcl|FitnessBrowser__Koxy:BWI76_RS23200 210 NGSSVCAIKGGRSVNTSMGFTPQSGVMMGTRSGDIDPSILPWLALHEGQTPEQLNQLLNNESGLLGVSGVS 280
                                             *********************************************************************** PP

                               TIGR00016 287 sDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlG 357
                                              D Rd++++ + gn +a+lAl ++++Ri+  ig+yi ++ g +Da++FtgGiGen+a  r  ++++l++lG
  lcl|FitnessBrowser__Koxy:BWI76_RS23200 281 HDYRDVEQAADGGNRRAALALALFAERIRATIGSYIMQMGG-IDALIFTGGIGENSARARSAICHNLNFLG 350
                                             ***************************************76.***************************** PP

                               TIGR00016 358 lkldlelnnaarsgkesvisteeskvkvlviptneelviaeDalrla 404
                                             l +d+e+n+    ++ ++i  e++ vkv+vi+tneel+ia+D++rla
  lcl|FitnessBrowser__Koxy:BWI76_RS23200 351 LSVDEEKNQ----HNATFIQAEHALVKVAVINTNEELMIARDVMRLA 393
                                             ********9....8899***************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (404 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: 11.43
//
[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