Alignments for a candidate for ackA in Lactobacillus delbrueckii ZN7a-9

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Lactobacillus delbrueckii ZN7a-9

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_002880041.1 B506_RS07515 acetate kinase

Query= BRENDA::Q9F1X7
         (397 letters)



>NCBI__GCF_000387565.1:WP_002880041.1
          Length = 395

 Score =  430 bits (1106), Expect = e-125
 Identities = 209/395 (52%), Positives = 290/395 (73%), Gaps = 3/395 (0%)

Query: 1   MSKIIAVNAGSSTLKFKLYEMPEENVLAEGVIERIALPASHVEIKYGDGKKYEKTTDVKN 60
           M KI+A+N+GSS+ K+K++ + +E+VLA G+ +RI +  S   +K  DG K+E   D+ N
Sbjct: 1   MDKILAINSGSSSFKYKMFSLADESVLASGLGDRIGIDGSTFSMKLADGTKHEAEVDLPN 60

Query: 61  HEQAIQILLDQLLDLDIIKEYSEINGVGHRVVAGGEYFDKSVVITPDVLKKIESLTELAP 120
            E A+Q LLD L +  +I +  EI GVGHR+V GGE F  S +I  + + K+  LT  AP
Sbjct: 61  QEVAVQTLLDWLKEYGVIADVKEIVGVGHRIVNGGELFPDSAIIDKENIHKVFDLTNYAP 120

Query: 121 LHEPANVLGIKAFKKVLPDIISVAVFDTAFHATLPEKNFLYSLPYEYYEKYSARKYGFHG 180
           LH PA   GI+AF K+LPD+  V VFDT+FH ++ E +++YSLPYEYYEKY ARKYG HG
Sbjct: 121 LHNPAEGHGIQAFMKILPDVPQVGVFDTSFHQSMDEVHYIYSLPYEYYEKYKARKYGAHG 180

Query: 181 IGNRYVSQRAAELLGKPAEDLKMIITHLGAGASICPVKNGKSFDTSMGFTPVTGITMATR 240
              RYVS +AAELLGK  +DLK+++ HLG+GAS+  VK+GK +DTSMGF+P+ G+TM TR
Sbjct: 181 TSVRYVSGKAAELLGKDLKDLKLVVCHLGSGASVTAVKDGKCYDTSMGFSPLAGVTMGTR 240

Query: 241 SGDVDPSLLAYVMEKEGMTDINEMIKVLNTKSGLLGISGVSADMREVEAAQATNPRAKVA 300
           SGDVDPS+L Y+M+KEG+TD NEMI +LN KSGLLG+SG+S+DMR++    + + RAK+A
Sbjct: 241 SGDVDPSVLQYIMKKEGITDFNEMIDILNHKSGLLGLSGISSDMRDIR--NSDDKRAKLA 298

Query: 301 REIYVNRIIRYVGAYLAEMGGADAIVFTAGVGENSITIRKEVAEGLNYFGIGVDNEKNDV 360
             +++NR++RYVG+Y+AEMGGADA+VFTAG+GE+   +R+ V + L++ G+  D+  N  
Sbjct: 299 DAVFINRVVRYVGSYIAEMGGADAVVFTAGIGEHDDEVREGVMKSLSFMGVDFDDAANKA 358

Query: 361 RGVVRDISAKDSKIKTLLVPTDEELMIVRDVQTLA 395
                 I+ +DSK+  L++PTDEELMI RDV  LA
Sbjct: 359 AN-EGFITKEDSKLAGLIIPTDEELMIERDVVRLA 392


Lambda     K      H
   0.316    0.135    0.372 

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: 488
Number of extensions: 21
Number of successful extensions: 3
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: 397
Length of database: 395
Length adjustment: 31
Effective length of query: 366
Effective length of database: 364
Effective search space:   133224
Effective search space used:   133224
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_002880041.1 B506_RS07515 (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.1083394.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.4e-145  468.4   0.2   9.4e-145  468.3   0.2    1.0  1  NCBI__GCF_000387565.1:WP_002880041.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000387565.1:WP_002880041.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  468.3   0.2  9.4e-145  9.4e-145       4     404 ..       2     392 ..       1     393 [. 0.98

  Alignments for each domain:
  == domain 1  score: 468.3 bits;  conditional E-value: 9.4e-145
                             TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 
                                            kil +n+Gsss k++++  ++ e+vl+sgl +ri +++++ +++  +++k+e++++ +++e av++ll+ lk
  NCBI__GCF_000387565.1:WP_002880041.1   2 DKILAINSGSSSFKYKMFSLAD-ESVLASGLGDRIGIDGSTFSMKLADGTKHEAEVDLPNQEVAVQTLLDWLK 73 
                                           69*******************7.999*****************999999************************ PP

                             TIGR00016  77 kdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknv 149
                                            +  ++ + +ei  +GHR+v+Gge f +s+i+++e ++k+ d++++APlHnpae +gi+a++  k+l+++++v
  NCBI__GCF_000387565.1:WP_002880041.1  74 -EYGVIADVKEIVGVGHRIVNGGELFPDSAIIDKENIHKVFDLTNYAPLHNPAEGHGIQAFM--KILPDVPQV 143
                                           .79***********************************************************..99******* PP

                             TIGR00016 150 avFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsa 222
                                            vFDt+fHq + e  y+Y+lPy++y++++ R+YG+HGts +yv+ +aa+ll+k l+dl+l+vcHlG Gasv+a
  NCBI__GCF_000387565.1:WP_002880041.1 144 GVFDTSFHQSMDEVHYIYSLPYEYYEKYKARKYGAHGTSVRYVSGKAAELLGKDLKDLKLVVCHLGSGASVTA 216
                                           ************************************************************************* PP

                             TIGR00016 223 vknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlgls.ldeieetlnkksGllgisglssDlRdild 294
                                           vk+Gk++dtsmG+ PL+G+ mGtRsGd+Dp++++y+++++g +  +e+ ++ln ksGllg+sg+ssD+Rdi +
  NCBI__GCF_000387565.1:WP_002880041.1 217 VKDGKCYDTSMGFSPLAGVTMGTRSGDVDPSVLQYIMKKEGITdFNEMIDILNHKSGLLGLSGISSDMRDIRN 289
                                           *****************************************98579*************************99 PP

                             TIGR00016 295 kkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnna 367
                                                +++aklA  v+++R+ +y+g+yia++ g  Da+vFt+GiGe + evre v+++l ++G+++d + n+ 
  NCBI__GCF_000387565.1:WP_002880041.1 290 SD---DKRAKLADAVFINRVVRYVGSYIAEMGG-ADAVVFTAGIGEHDDEVREGVMKSLSFMGVDFDDAANK- 357
                                           87...5689**********************77.9**********************************999. PP

                             TIGR00016 368 arsgkesvisteeskvkvlviptneelviaeDalrla 404
                                               +e++i++e+sk+  l+ipt+eel+i +D++rla
  NCBI__GCF_000387565.1:WP_002880041.1 358 --AANEGFITKEDSKLAGLIIPTDEELMIERDVVRLA 392
                                           ..7789*****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (395 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: 30.23
//
[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 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