Alignments for a candidate for ackA in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Herbaspirillum seropedicae SmR1

Align Acetate kinase; EC 2.7.2.1; Acetokinase (uncharacterized)
to candidate HSERO_RS01305 HSERO_RS01305 acetate kinase

Query= curated2:Q1QPW6
         (404 letters)



>FitnessBrowser__HerbieS:HSERO_RS01305
          Length = 397

 Score =  311 bits (798), Expect = 2e-89
 Identities = 182/402 (45%), Positives = 247/402 (61%), Gaps = 19/402 (4%)

Query: 4   ILVVNAGSSSVKFQVFSAEGEGKLLRQIKGQVDGIGSRP---RLRASGADNEPLADRAYP 60
           +L  NAGSS++K  VF  +G  +  +  +GQ+D +   P   RL   G  +E        
Sbjct: 5   LLTFNAGSSTIKLGVFRLDG-ARARKIGQGQLD-LHLAPLKLRLEIDGERSE-------- 54

Query: 61  IESVSDVPAAMGVAGGWLRDELRISPM-----AVGHRVVHGGPDYDRPVLIDHGVVARLE 115
           +E  +D  AAM      +  +L +        AVGHRVVHGG    + V +D  +   LE
Sbjct: 55  VEIDADPAAAMDRVLEQVLHQLEVGHAQGELCAVGHRVVHGGLHLAQAVRLDDAIETELE 114

Query: 116 RFVALAPLHQPNNLDPIRSLLANFPALPQVACFDTAFHRTHDAVADYYAIPYQFYVEGVR 175
               LAPLHQP NL  IR++    P LPQ A FDTAFH + DA+A  +A+P + + EGV 
Sbjct: 115 NLAPLAPLHQPQNLRLIRAIARLRPGLPQTASFDTAFHASQDALARRFALPRRLHEEGVL 174

Query: 176 RYGFHGLSYEYVAKTLPHVAPEIAKGRVIVAHLGSGASMCALKGGRSIESTMGFTALDGL 235
           RYGFHG+SY YVA  +   A   A  RV+VAHLG+GAS+CAL  GRS++++ GF+ LDG+
Sbjct: 175 RYGFHGISYSYVAAEMRRQALPEAHARVVVAHLGNGASLCALHAGRSVDASTGFSTLDGV 234

Query: 236 PMGTRPGQIDPGVVLYLVSEKGMSPAKAQDFLYRDCGLKGLSGVSNDMRELEASEDPKAK 295
           PMGTR G +D GV+LYL+  +GMS  + +D LY   GL G+SG+S D+R L+ S+D  A+
Sbjct: 235 PMGTRCGALDAGVLLYLL-RQGMSLDELEDLLYHRSGLLGVSGLSADVRSLQQSQDSAAR 293

Query: 296 LAVDYFVYRVGLNAGMLAAALQGLDAFVFTAGIGENSMRIRARIADQLAWLGVTLDPTQN 355
            A+D F  R    A  LA+ L G+DA VFTAGIGE+   +RA I ++L WLGV LDP  N
Sbjct: 294 EALDLFALRCAGEAARLASTLGGIDALVFTAGIGEHDAAMRAAICERLGWLGVRLDPQAN 353

Query: 356 SRHARLISGSDSRIPVYVIPTDEELMIAQHTLSLLLDRSSSS 397
           + HA  IS +DS + VYVIPT+EE +IA    +LLL  ++ +
Sbjct: 354 AAHAGRISRADSAVSVYVIPTNEEQVIADDAAALLLTSATGT 395


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: 441
Number of extensions: 16
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: 404
Length of database: 397
Length adjustment: 31
Effective length of query: 373
Effective length of database: 366
Effective search space:   136518
Effective search space used:   136518
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 HSERO_RS01305 HSERO_RS01305 (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.5636.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
    9.4e-99  316.8   0.0    1.1e-98  316.6   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS01305  HSERO_RS01305 acetate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS01305  HSERO_RS01305 acetate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  316.6   0.0   1.1e-98   1.1e-98       4     403 ..       3     387 ..       1     389 [. 0.91

  Alignments for each domain:
  == domain 1  score: 316.6 bits;  conditional E-value: 1.1e-98
                                  TIGR00016   4 kkilvlnaGssslkfalldaense.kvllsglverikleeariktvedgekkeeeklaiedheeavkk 70 
                                                +++l  naGss +k  ++   +++ +++ +g  +    +  ++    dge+ e e+   +d ++a+++
  lcl|FitnessBrowser__HerbieS:HSERO_RS01305   3 RLLLTFNAGSSTIKLGVFRLDGARaRKIGQGQLDLHLAP-LKLRLEIDGERSEVEID--ADPAAAMDR 67 
                                                578999************999854145789988865554.44555566655555444..577899*** PP

                                  TIGR00016  71 llntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavl 138
                                                +l+++ ++ ++ + + e+ ++GHRvvhGg +++++v ++d +  +++++++lAPlH p++l  i+a+ 
  lcl|FitnessBrowser__HerbieS:HSERO_RS01305  68 VLEQVLHQLEVGHAQGELCAVGHRVVHGGLHLAQAVRLDDAIETELENLAPLAPLHQPQNLRLIRAIA 135
                                                ******9************************************************************* PP

                                  TIGR00016 139 klkvllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkpldd 206
                                                     +  ++ a FDtafH      a  +alP++l+ e gv rYGfHG+s++yv+ ++ +    p+++
  lcl|FitnessBrowser__HerbieS:HSERO_RS01305 136 --RLRPGLPQTASFDTAFHASQDALARRFALPRRLH-EEGVLRYGFHGISYSYVAAEMRRQ-ALPEAH 199
                                                ..5556667***********************7765.66999*************998765.56789* PP

                                  TIGR00016 207 lnlivcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetln 274
                                                 +++v+HlGnGas++a++ G+s+d s G+  L+G+ mGtR+G +D +++ yl   +g+slde+e++l 
  lcl|FitnessBrowser__HerbieS:HSERO_RS01305 200 ARVVVAHLGNGASLCALHAGRSVDASTGFSTLDGVPMGTRCGALDAGVLLYLLR-QGMSLDELEDLLY 266
                                                ****************************************************86.79*********** PP

                                  TIGR00016 275 kksGllgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGena 342
                                                 +sGllg+sgls+D+R + + +   +  a+ Al++++ R a   ++ +++l g +Da+vFt+GiGe +
  lcl|FitnessBrowser__HerbieS:HSERO_RS01305 267 HRSGLLGVSGLSADVRSLQQSQ---DSAAREALDLFALRCAGEAARLASTLGG-IDALVFTAGIGEHD 330
                                                ******************9988...45689*********************66.************** PP

                                  TIGR00016 343 aevrelvleklevlGlkldlelnnaarsgkesvisteeskvkvlviptneelviaeDalrl 403
                                                a +r+ ++e+l  lG++ld++ n      + + is  +s+v v+viptnee via Da+ l
  lcl|FitnessBrowser__HerbieS:HSERO_RS01305 331 AAMRAAICERLGWLGVRLDPQANA----AHAGRISRADSAVSVYVIPTNEEQVIADDAAAL 387
                                                *********************999....77889************************9876 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: 10.30
//
[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