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.29545.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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.67
//
[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:

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:

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:

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:

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