Alignments for a candidate for ackA in Psychromonas ingrahamii 37

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Psychromonas ingrahamii 37

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_011771550.1 PING_RS17085 acetate kinase

Query= BRENDA::E3W769
         (401 letters)



>NCBI__GCF_000015285.1:WP_011771550.1
          Length = 404

 Score =  535 bits (1378), Expect = e-157
 Identities = 267/399 (66%), Positives = 320/399 (80%), Gaps = 1/399 (0%)

Query: 1   MSDKLVLVLNCGSSSLKFAIIDAQSGDDKISGLAECFGLEDSRIKWKFNGGKNEAKLGAF 60
           M++KLVLVLNCGSSSLKFA+I+A +G + +SGLAECF L ++RIKWK  G K    L  +
Sbjct: 1   MNNKLVLVLNCGSSSLKFAVINADNGGEIMSGLAECFNLPEARIKWKMAGTKKSTSLPPY 60

Query: 61  TAHREAVEFFIVNNILAEHPELAAQIKAIGHRIVHGGEKFTRSVIITPEVIQGIEDCASL 120
           +AH  A+ F IV  I+ +   L  Q  A+GHRIVHGGE+FT SVII   V++GIE C+SL
Sbjct: 61  SAHSAAISF-IVEEIIKKEAGLTEQFVAVGHRIVHGGERFTESVIIDDHVLEGIEQCSSL 119

Query: 121 APLHNPAHLIGIRAAIASFPQLPQVTVFDTAFHQTMPEKAYIYALPYKLYREHSIRRYGM 180
           APLHNPAH +GIRAA  +FP LPQV VFDTAFHQTMP KA++YALPY LY+E+SIRRYGM
Sbjct: 120 APLHNPAHALGIRAAQVAFPALPQVAVFDTAFHQTMPAKAFMYALPYHLYKEYSIRRYGM 179

Query: 181 HGTSHFYVCREAAKVLGKDVKDINVICAHLGNGASVAAIKGGKSVDTSMGLTPLEGLVMG 240
           HGTS+ +V  EAAK+L K V D+NVICAHLGNGASV AIK G+SVDTSMGLTPL+GLVMG
Sbjct: 180 HGTSNLFVTHEAAKILNKPVDDLNVICAHLGNGASVTAIKKGQSVDTSMGLTPLDGLVMG 239

Query: 241 TRCGDLDPSIIFHLVKQLGYTLDEVNNLLNKQSGLLGISELTNDCRGIEEGYHDGHKGAT 300
           TRCGDLDPSII +L+ +LGY+++ V  +L KQSGLLGIS +++D R I  GY  G K AT
Sbjct: 240 TRCGDLDPSIIEYLITRLGYSIEGVMEILQKQSGLLGISGISSDFREIIAGYEQGSKRAT 299

Query: 301 LALDIFCYRLAKYIASYTVPLGRLDAIIFTGGIGENSNLIREKVLNLLEIFNFKVDDILN 360
           LA+D+F YRLAKYIASY VPLG +DAIIFTGGIGENS L+R KVL LL IF ++VD   N
Sbjct: 300 LAIDMFIYRLAKYIASYAVPLGHIDAIIFTGGIGENSPLVRSKVLELLTIFGYQVDGEKN 359

Query: 361 KAARFGQQGVITQAGTPIAMVIPTNEEWVIAEDAIKLIT 399
           KAA  G QG+IT AG+PIAMVIPTNEEWVIA+D+ KL++
Sbjct: 360 KAAILGNQGIITIAGSPIAMVIPTNEEWVIAQDSAKLVS 398


Lambda     K      H
   0.321    0.139    0.409 

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: 507
Number of extensions: 18
Number of successful extensions: 2
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: 404
Length adjustment: 31
Effective length of query: 370
Effective length of database: 373
Effective search space:   138010
Effective search space used:   138010
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 WP_011771550.1 PING_RS17085 (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.3647558.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.9e-163  527.8   0.1     9e-163  527.6   0.1    1.0  1  NCBI__GCF_000015285.1:WP_011771550.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015285.1:WP_011771550.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  527.6   0.1    9e-163    9e-163       1     404 [.       1     397 [.       1     398 [. 0.97

  Alignments for each domain:
  == domain 1  score: 527.6 bits;  conditional E-value: 9e-163
                             TIGR00016   1 mkskkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkklln 73 
                                           m++k++lvln+Gssslkfa+++a n+ ++ +sgl+e+++l+earik+++ g kk++     ++h++a++++++
  NCBI__GCF_000015285.1:WP_011771550.1   1 MNNKLVLVLNCGSSSLKFAVINADNGGEI-MSGLAECFNLPEARIKWKMAGTKKSTSLPPYSAHSAAISFIVE 72 
                                           57899*******************99988.******************************************* PP

                             TIGR00016  74 tlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllka 146
                                           ++ k++    ++++  ++GHR+vhGge+ftesvi++d+vl++i++ s+lAPlHnpa++ gi+a++     +  
  NCBI__GCF_000015285.1:WP_011771550.1  73 EIIKKE--AGLTEQFVAVGHRIVHGGERFTESVIIDDHVLEGIEQCSSLAPLHNPAHALGIRAAQ--VAFPAL 141
                                           ***755..7888999**************************************************..677778 PP

                             TIGR00016 147 knvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGas 219
                                           ++vavFDtafHqt+p +a++YalPy+lyke+ +RrYG+HGts  +vt++aak+lnkp+ddln+i +HlGnGas
  NCBI__GCF_000015285.1:WP_011771550.1 142 PQVAVFDTAFHQTMPAKAFMYALPYHLYKEYSIRRYGMHGTSNLFVTHEAAKILNKPVDDLNVICAHLGNGAS 214
                                           8************************************************************************ PP

                             TIGR00016 220 vsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdi 292
                                           v+a+k+G+s+dtsmGltPL+GlvmGtR+Gd+Dp+ii yl ++lg s++ + e+l+k+sGllgisg+ssD+R+i
  NCBI__GCF_000015285.1:WP_011771550.1 215 VTAIKKGQSVDTSMGLTPLDGLVMGTRCGDLDPSIIEYLITRLGYSIEGVMEILQKQSGLLGISGISSDFREI 287
                                           ************************************************************************* PP

                             TIGR00016 293 ldkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldleln 365
                                           ++ +e+g ++a+lA++++++R+akyi++y+  l g++Dai+FtgGiGen+  vr +vle l ++G ++d e+n
  NCBI__GCF_000015285.1:WP_011771550.1 288 IAGYEQGSKRATLAIDMFIYRLAKYIASYAVPL-GHIDAIIFTGGIGENSPLVRSKVLELLTIFGYQVDGEKN 359
                                           *********************************.56************************************* PP

                             TIGR00016 366 naarsgkesvisteeskvkvlviptneelviaeDalrla 404
                                           +aa  g++++i+   s   ++viptnee+via+D+++l+
  NCBI__GCF_000015285.1:WP_011771550.1 360 KAAILGNQGIITIAGSP-IAMVIPTNEEWVIAQDSAKLV 397
                                           *99********977666.5799*************9986 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: 00:00:00.00
# Mc/sec: 18.22
//
[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 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