Alignments for a candidate for ackA in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Phaeobacter inhibens BS107

Align propionate kinase (EC 2.7.2.15) (characterized)
to candidate GFF2838 PGA1_c28840 acetate kinase AckA

Query= BRENDA::O06961
         (402 letters)



>FitnessBrowser__Phaeo:GFF2838
          Length = 386

 Score =  242 bits (617), Expect = 2e-68
 Identities = 155/384 (40%), Positives = 218/384 (56%), Gaps = 14/384 (3%)

Query: 7   VLVINCGSSSIKFSVLDVATCDVLMAGIADGMNTENAFLSINGDKPINLAHSNYEDALKA 66
           +L++N GSSSIKF++ D    +  +AG+A+G+ T  + L I  D   +     + +AL A
Sbjct: 9   ILILNAGSSSIKFAIFDT-DLNQRLAGLAEGIGTPQSRLRI-ADTSRDSQLPTHAEALAA 66

Query: 67  IAFELEKRDLTDS-VALIGHRIAHGGELFTQSVIITDEIIDNIRRVSPLAPLHNYANLSG 125
           I   L    L  + +A +GHR+ HGG   T+ V IT EI   I   +PLAPLHN  +L+ 
Sbjct: 67  ILAALPDHGLDPTQLAAVGHRVVHGGRKLTKPVRITPEIRAEIADCTPLAPLHNPHSLAA 126

Query: 126 IDAARHLFPAVRQVAVFDTSFHQTLAPEAYLYGLPWEYFSSLGVRRYGFHGTSHRYVSRR 185
           ID      P + Q A FDTSFH T    A  Y +P     + G+RRYGFHG S+  + RR
Sbjct: 127 IDTMATTAPDLPQFASFDTSFHATNPEVATRYAIP-RVEETKGIRRYGFHGLSYASLVRR 185

Query: 186 AYELLDLDEKDSGLIVAHLGNGASICAVRNGQSVDTSMGMTPLEGLMMGTRSGDVDFGAM 245
             E+       S L+  HLGNGAS+CA+RNGQSV T+MG +PL+GL MGTRSG +D  A+
Sbjct: 186 LPEISGA-ALPSRLLAFHLGNGASLCAIRNGQSVATTMGYSPLDGLTMGTRSGGIDANAV 244

Query: 246 AWIAKETGQTLSDLERVVNKESGLLGISGLSSDLRVLEKAWHEGHERARLAIKTFVHRIA 305
             + ++ G  L   + ++N ESGLLG+SG  SD+R L     +    +  AI+ F +   
Sbjct: 245 LRLVEDNG--LDRTKAILNNESGLLGLSGGKSDMRNL---MLDPSADSAFAIEHFCYWSL 299

Query: 306 RHIAGHAASLHRLDGIIFTGGIGENSVLIRQLVIEHLGVLGLTLDVEMNKQPNSHGERII 365
           RH     A++  LD I FTGGIGEN+V +R  ++  L  +G  +DV+ N    S     +
Sbjct: 300 RHAGSLIAAMEGLDAIAFTGGIGENAVGVRARILRGLEWIGARMDVDANHARKSR----L 355

Query: 366 SANPSQVICAVIPTNEEKMIALDA 389
            A  S+V   V+   EE+ IA+DA
Sbjct: 356 HAGSSKVAIWVVEAEEERQIAMDA 379


Lambda     K      H
   0.320    0.137    0.397 

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: 380
Number of extensions: 25
Number of successful extensions: 7
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: 402
Length of database: 386
Length adjustment: 31
Effective length of query: 371
Effective length of database: 355
Effective search space:   131705
Effective search space used:   131705
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 GFF2838 PGA1_c28840 (acetate kinase AckA)
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.7641.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   2.8e-107  344.9   0.0   3.2e-107  344.7   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF2838  PGA1_c28840 acetate kinase AckA


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF2838  PGA1_c28840 acetate kinase AckA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  344.7   0.0  3.2e-107  3.2e-107       4     403 ..       7     382 ..       4     384 .. 0.92

  Alignments for each domain:
  == domain 1  score: 344.7 bits;  conditional E-value: 3.2e-107
                          TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkkdk 79 
                                          il+lnaGsss+kfa++d+   ++  l gl+e i  +++r+ +  +     +   + + h+ea++++l +l  d+
  lcl|FitnessBrowser__Phaeo:GFF2838   7 DNILILNAGSSSIKFAIFDTDL-NQR-LAGLAEGIGTPQSRLRIADT-----SRDSQLPTHAEALAAILAALP-DH 74 
                                        679****************994.565.69***********7664333.....35678899*************.67 PP

                          TIGR00016  80 kilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknvavFDta 155
                                         +  +  ++a++GHRvvhGg k+t+ v +t e+ ++i+d ++lAPlHnp  l +i+++   ++ ++ ++ a FDt+
  lcl|FitnessBrowser__Phaeo:GFF2838  75 GL--DPTQLAAVGHRVVHGGRKLTKPVRITPEIRAEIADCTPLAPLHNPHSLAAIDTMA--TTAPDLPQFASFDTS 146
                                        65..5679*************************************************99..899999********* PP

                          TIGR00016 156 fHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsavknGksidt 231
                                        fH t pe a  Ya+P ++++ +g+RrYGfHG+s+  + +r+ ++ +  +  ++l+  HlGnGas++a++nG+s+ t
  lcl|FitnessBrowser__Phaeo:GFF2838 147 FHATNPEVATRYAIP-RVEETKGIRRYGFHGLSYASLVRRLPEISGA-ALPSRLLAFHLGNGASLCAIRNGQSVAT 220
                                        ***************.8999************************998.56889*********************** PP

                          TIGR00016 232 smGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkkeegneeaklAl 307
                                        +mG  PL+Gl mGtRsG iD  ++  l e +g  ld  + +ln +sGllg+sg  sD+R+++ ++     +++ A+
  lcl|FitnessBrowser__Phaeo:GFF2838 221 TMGYSPLDGLTMGTRSGGIDANAVLRLVEDNG--LDRTKAILNNESGLLGLSGGKSDMRNLMLDP---SADSAFAI 291
                                        *********************99998888766..678899*********************9999...45789*** PP

                          TIGR00016 308 kvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaarsgkesvisteeskv 383
                                        + +++   ++ g+ ia++eg lDai FtgGiGena+ vr+++l++le +G ++d + n+     ++s +    skv
  lcl|FitnessBrowser__Phaeo:GFF2838 292 EHFCYWSLRHAGSLIAAMEG-LDAIAFTGGIGENAVGVRARILRGLEWIGARMDVDANH----ARKSRLHAGSSKV 362
                                        ******************99.************************************99....4555667789*** PP

                          TIGR00016 384 kvlviptneelviaeDalrl 403
                                         + v++ +ee  ia Da  l
  lcl|FitnessBrowser__Phaeo:GFF2838 363 AIWVVEAEEERQIAMDAQTL 382
                                        ****************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (386 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.23
//
[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