Alignments for a candidate for ackA in Sinorhizobium fredii NGR234

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Sinorhizobium fredii NGR234

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_015887456.1 NGR_RS06510 acetate kinase

Query= BRENDA::P0CW04
         (408 letters)



>NCBI__GCF_000018545.1:WP_015887456.1
          Length = 394

 Score =  251 bits (641), Expect = 3e-71
 Identities = 162/401 (40%), Positives = 229/401 (57%), Gaps = 18/401 (4%)

Query: 3   VLVINAGSSSLKYQLIDMTNESALAIGLCERI-GIDNSIITQKRFDGKKLEKQTDLPNHK 61
           +LV+NAGSSSLK+Q+  +     +A GL  ++ G    I T+ R   K  E  T L +  
Sbjct: 4   LLVVNAGSSSLKFQVFGI-----VAAGLARQVRGQIGGIGTRPRLQAKGAEG-TVLVDQS 57

Query: 62  IALEEV--VKALTDSEFGVIKSMD--EINAVGHRVVHGGEKFNSSALINEGVEQAIKDCF 117
            A E V  + A   +    + ++D  E+ A+GHRVVHGG  +    LI+  V   +    
Sbjct: 58  YAAEAVRDLPAAIAAAREWLLTLDGLELRAIGHRVVHGGPDYAQPVLIDATVLDRLASYQ 117

Query: 118 ELAPLHNPPNMMGISSCQEIMPGVPMVAVFDTAFHHTIPPYAYMYALPYELYEKYGIRKY 177
           +LAPLH P N+  I    EI P VP VA FDTAFH     +   YALP   Y++ GIR+Y
Sbjct: 118 DLAPLHQPNNLAPIRLAMEINPDVPQVACFDTAFHRGHAEHTDCYALPRTFYDQ-GIRRY 176

Query: 178 GFHGTSHFYVAKRAAAMLGKPEQDVKVITCHLGNGSSITAVKGGKSIETTMGFTPLEGVA 237
           GFHG S+ Y+A+R    +       KVI  HLG+G+S+ A+  G+SIE+TMGFT L+G+ 
Sbjct: 177 GFHGLSYEYIAERLRE-IAPGAAGGKVIVAHLGSGASMCALSDGRSIESTMGFTALDGLP 235

Query: 238 MGTRCGSIDPAVVPFIMEKEGLSTREIDTLMNKKSGVLGVSSLSNDFRDLDEAASKGNQK 297
           MGTR G +DP VV +++ ++G+S   +  L+   +G+ G+S +SND R+L    +  + +
Sbjct: 236 MGTRPGQLDPGVVLYLISEKGMSADAVSDLLYHDAGLKGLSGISNDMREL---LASDDPR 292

Query: 298 AELALEIFAYKIKKVIGEYIAVLNGVDAIVFTAGIGENSATIRKRILADLDGIGIKIDEE 357
           A  A+  F ++     G   A L G+DA VFTAG+GENSA IR RI   L  +G ++D  
Sbjct: 293 AAFAIAHFVHRCMLNAGMLAAALGGLDAFVFTAGVGENSAPIRARIAEGLAWLGAELDPT 352

Query: 358 KNKIRGQEIDISTPDATVRVLVIPTNEELTIARDTKEICET 398
            N   G    IST  + V + VIPT+EEL IAR T  +  T
Sbjct: 353 ANDAGGPL--ISTATSRVALHVIPTDEELMIARHTLALIST 391


Lambda     K      H
   0.317    0.135    0.380 

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: 375
Number of extensions: 12
Number of successful extensions: 6
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: 408
Length of database: 394
Length adjustment: 31
Effective length of query: 377
Effective length of database: 363
Effective search space:   136851
Effective search space used:   136851
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_015887456.1 NGR_RS06510 (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.1810837.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.8e-106  342.2   0.0   2.1e-106  342.0   0.0    1.0  1  NCBI__GCF_000018545.1:WP_015887456.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000018545.1:WP_015887456.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  342.0   0.0  2.1e-106  2.1e-106       5     404 ..       3     389 ..       1     390 [. 0.90

  Alignments for each domain:
  == domain 1  score: 342.0 bits;  conditional E-value: 2.1e-106
                             TIGR00016   5 kilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkk 77 
                                            +lv+naGssslkf+++        l++ +  +i   ++r   ++  + + +  ++ +  +eav+ l  ++ +
  NCBI__GCF_000018545.1:WP_015887456.1   3 ALLVVNAGSSSLKFQVFGIVA--AGLARQVRGQIGGIGTRPR-LQAKGAEGTVLVDQSYAAEAVRDLPAAIAA 72 
                                           689**************9994..3344555555544444333.444455667788888889999999999998 PP

                             TIGR00016  78 dkkilkels..eialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkakn 148
                                            ++ l +l+  e+++iGHRvvhGg ++++ v++++ vl++++   +lAPlH p++l  i+ ++  ++ +++++
  NCBI__GCF_000018545.1:WP_015887456.1  73 AREWLLTLDglELRAIGHRVVHGGPDYAQPVLIDATVLDRLASYQDLAPLHQPNNLAPIRLAM--EINPDVPQ 143
                                           544444443238999**********************************************99..999***** PP

                             TIGR00016 149 vavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvs 221
                                           va+FDtafH+  +e++  YalP+ +y ++g+RrYGfHG+s++y+++r+ ++    ++  ++iv+HlG Gas++
  NCBI__GCF_000018545.1:WP_015887456.1 144 VACFDTAFHRGHAEHTDCYALPRTFY-DQGIRRYGFHGLSYEYIAERLREIAPG-AAGGKVIVAHLGSGASMC 214
                                           **********************8877.57********************99877.7899************** PP

                             TIGR00016 222 avknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdild 294
                                           a+ +G+si+ +mG+t L+Gl mGtR G++Dp+++ yl +++g+s+d++ ++l  ++Gl g+sg+s+D+R++l+
  NCBI__GCF_000018545.1:WP_015887456.1 215 ALSDGRSIESTMGFTALDGLPMGTRPGQLDPGVVLYLISEKGMSADAVSDLLYHDAGLKGLSGISNDMRELLA 287
                                           ***********************************************************************98 PP

                             TIGR00016 295 kkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnna 367
                                                + +a+ A+  +vhR     g  +a+l g lDa vFt+G+Gen+a +r+++ e+l+ lG +ld+  n  
  NCBI__GCF_000018545.1:WP_015887456.1 288 SD---DPRAAFAIAHFVHRCMLNAGMLAAALGG-LDAFVFTAGVGENSAPIRARIAEGLAWLGAELDPTAND- 355
                                           87...7899**********************66.***********************************999. PP

                             TIGR00016 368 arsgkesvisteeskvkvlviptneelviaeDalrla 404
                                                  +ist  s+v + vipt+eel+ia+ +l l+
  NCBI__GCF_000018545.1:WP_015887456.1 356 ---AGGPLISTATSRVALHVIPTDEELMIARHTLALI 389
                                           ...7789***********************9988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (394 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: 00:00:00.00
# Mc/sec: 25.85
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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