Alignments for a candidate for ackA in Pseudomonas stutzeri A1501

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Pseudomonas stutzeri A1501

Align Acetate kinase; EC 2.7.2.1; Acetokinase (uncharacterized)
to candidate WP_011911909.1 PST_RS03550 acetate/propionate family kinase

Query= curated2:Q1QPW6
         (404 letters)



>NCBI__GCF_000013785.1:WP_011911909.1
          Length = 402

 Score =  373 bits (958), Expect = e-108
 Identities = 194/389 (49%), Positives = 266/389 (68%), Gaps = 4/389 (1%)

Query: 4   ILVVNAGSSSVKFQVFSAE-GEGKLLRQIKGQVDGIGSRPRLRASGADNEPLADRAYPIE 62
           I+ VNAGSSS+K  +FS   GE +     +G++DGIG  PRL+   AD   + D ++  E
Sbjct: 9   IVTVNAGSSSIKTGLFSGRRGEDQPRLLARGKLDGIGVAPRLQVVMADGTIMQDTSFEPE 68

Query: 63  SVSDVPAAMGVAGGWLRDELRISP-MAVGHRVVHGGPDYDRPVLIDHGVVARLERFVALA 121
            ++++ AA       L + L+  P + +GHRVVHGG D+  PV +DH  +ARL+    LA
Sbjct: 69  QIANMQAAFQQIYRVLEEGLQDRPPVLIGHRVVHGGMDFSAPVRVDHTTLARLKTLEPLA 128

Query: 122 PLHQPNNLDPIRSLLANFPALPQVACFDTAFHRTHDAVADYYAIPYQFYVEGVRRYGFHG 181
           PLHQP+NL  I + L + P LPQ+ACFDTAFH   + ++  + +PY  Y +GVRRYGFHG
Sbjct: 129 PLHQPHNLAAIHAALEHDPQLPQIACFDTAFHAGRNEISQLFGLPYALYEQGVRRYGFHG 188

Query: 182 LSYEYVAKTLPHVAPEIAKGRVIVAHLGSGASMCALKGGRSIESTMGFTALDGLPMGTRP 241
           LS+EYV++ L    PE+A G++++AHLG+G+S+CA++ GRSIE T GF+ALDGLPMG+R 
Sbjct: 189 LSFEYVSQRLIDKTPELATGKLVIAHLGNGSSLCAIEAGRSIEMTTGFSALDGLPMGSRC 248

Query: 242 GQIDPGVVLYLVSEKGMSPAKAQDFLYRDCGLKGLSGVSNDMRELEASEDPKAKLAVDYF 301
           G +DPGV+LYL+ + G+S  + +  LYR  GL G+SGVS+DMR+L AS +P+A LA+DY+
Sbjct: 249 GAVDPGVLLYLLGQ-GISVDELEKLLYRQSGLLGISGVSSDMRKLRASNEPRAALAIDYY 307

Query: 302 VYRVGLNAGMLAAALQGLDAFVFTAGIGENSMRIRARIADQLAWL-GVTLDPTQNSRHAR 360
            YR+    G LA  L GLDA VFTAGIGE    +RA++   LA L G+ LD   N R+A 
Sbjct: 308 AYRIAQEVGRLATCLGGLDALVFTAGIGEKDAELRAQVLQHLAPLFGLQLDDAANRRNAE 367

Query: 361 LISGSDSRIPVYVIPTDEELMIAQHTLSL 389
           LISG+ S   V+VIPTDEE +IA+H   L
Sbjct: 368 LISGTSSTRSVWVIPTDEESIIARHAWKL 396


Lambda     K      H
   0.320    0.137    0.403 

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: 466
Number of extensions: 20
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: 404
Length of database: 402
Length adjustment: 31
Effective length of query: 373
Effective length of database: 371
Effective search space:   138383
Effective search space used:   138383
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_011911909.1 PST_RS03550 (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.24113.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-105  339.2   0.0   1.7e-105  339.0   0.0    1.0  1  lcl|NCBI__GCF_000013785.1:WP_011911909.1  PST_RS03550 acetate/propionate f


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000013785.1:WP_011911909.1  PST_RS03550 acetate/propionate family kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  339.0   0.0  1.7e-105  1.7e-105       3     404 ..       6     397 ..       4     398 .. 0.91

  Alignments for each domain:
  == domain 1  score: 339.0 bits;  conditional E-value: 1.7e-105
                                 TIGR00016   3 skkilvlnaGssslkfalldaensekv...llsglverikleeariktvedg...ekkeeeklaiedhe 65 
                                               +++i+ +naGsss+k  l+  + +e     l++g  + i ++     ++ dg   ++++ e  +i++ +
  lcl|NCBI__GCF_000013785.1:WP_011911909.1   6 DELIVTVNAGSSSIKTGLFSGRRGEDQprlLARGKLDGIGVAPRLQVVMADGtimQDTSFEPEQIANMQ 74 
                                               678999**************99887766669**********9986655555522245566778899999 PP

                                 TIGR00016  66 eavkkllntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegi 134
                                               +a +++ + l++    l++     liGHRvvhGg +f+  v v++ +l+++k + +lAPlH p +l +i
  lcl|NCBI__GCF_000013785.1:WP_011911909.1  75 AAFQQIYRVLEE--G-LQDRP-PVLIGHRVVHGGMDFSAPVRVDHTTLARLKTLEPLAPLHQPHNLAAI 139
                                               999999999995..2.34444.459******************************************** PP

                                 TIGR00016 135 eavlklkvllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkp 203
                                               +a+l  +  ++ +++a+FDtafH   +e + l++lPy ly+ +gvRrYGfHG+s++yv+qr+ ++    
  lcl|NCBI__GCF_000013785.1:WP_011911909.1 140 HAAL--EHDPQLPQIACFDTAFHAGRNEISQLFGLPYALYE-QGVRRYGFHGLSFEYVSQRLIDKTPE- 204
                                               ***9..8899999*************************996.69*****************9999877. PP

                                 TIGR00016 204 lddlnlivcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieet 272
                                               l+  +l+++HlGnG+s++a++ G+si+ + G+  L+Gl mG+R+G +Dp+++ yl   +g s+de+e++
  lcl|NCBI__GCF_000013785.1:WP_011911909.1 205 LATGKLVIAHLGNGSSLCAIEAGRSIEMTTGFSALDGLPMGSRCGAVDPGVLLYLLG-QGISVDELEKL 272
                                               9999***************************************************86.69********* PP

                                 TIGR00016 273 lnkksGllgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGen 341
                                               l ++sGllgisg+ssD+R++ +     + +a+lA++ y++Ria+ +g+ ++ l g lDa+vFt+GiGe 
  lcl|NCBI__GCF_000013785.1:WP_011911909.1 273 LYRQSGLLGISGVSSDMRKLRASN---EPRAALAIDYYAYRIAQEVGRLATCLGG-LDALVFTAGIGEK 337
                                               *******************98877...778***********************66.************* PP

                                 TIGR00016 342 aaevrelvlekle.vlGlkldlelnnaarsgkesvisteeskvkvlviptneelviaeDalrla 404
                                               +ae+r++vl++l+ ++Gl+ld + n      +  +is + s+  v vipt+ee++ia+ a++l 
  lcl|NCBI__GCF_000013785.1:WP_011911909.1 338 DAELRAQVLQHLApLFGLQLDDAANR----RNAELISGTSSTRSVWVIPTDEESIIARHAWKLY 397
                                               ************8467*****99998....67789**************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (402 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: 8.19
//
[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