Alignments for a candidate for ackA in Neptunomonas antarctica S3-22

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Neptunomonas antarctica S3-22

Align Acetate kinase; EC 2.7.2.1; Acetokinase (uncharacterized)
to candidate WP_054340820.1 Nant_RS06470 acetate/propionate family kinase

Query= curated2:B8EIS2
         (404 letters)



>NCBI__GCF_001305295.1:WP_054340820.1
          Length = 395

 Score =  343 bits (879), Expect = 7e-99
 Identities = 181/402 (45%), Positives = 253/402 (62%), Gaps = 20/402 (4%)

Query: 5   VITLNAGSSSIKFALFREGLTQEGSAKELTPM-AIGLAEMVGEERRITVHDGAGAKIY-- 61
           ++T+N GSSS+K  LF+    +E      TP+    L  ++GE R IT+ D +G KI   
Sbjct: 4   ILTINGGSSSLKCTLFKTASHEE------TPIYQFKLGNILGEPR-ITLSDSSGNKITPP 56

Query: 62  -----EVKRTEHVDAPFHAEALRRILAWRQSAFPDAEVVAAGHRVVHGGVHYSAPVIVTD 116
                 V + E      H  ALR +L W +   P   + A GHRVVHGG  ++APV++  
Sbjct: 57  TIDISHVPKNER-----HKAALRTVLNWLEEHAPHLRLTAFGHRVVHGGELFTAPVLIDS 111

Query: 117 EVLKYLHTLIPLAPLHEPYNIAGILGAREAWPHVEQVACFDTAFHRTHPFVNDVFALPRR 176
             +  L   IPLAPLH+PYN+  I   +   P + QVACFDT FH   P V   +A+PR+
Sbjct: 112 PTMTALEAFIPLAPLHQPYNLLLIEACQALKPDLPQVACFDTTFHVGQPAVERHYAIPRK 171

Query: 177 FYDEGVRRYGFHGLSYEYIVRRLREIAPLHAAGRVVVAHLGNGASMCAIRDGLSVASSMG 236
           +  EG+ RYGFHGLSYEYI + L+ ++   +  + +V HLG GASMCAI  G S+AS+MG
Sbjct: 172 YTKEGIHRYGFHGLSYEYIQKTLKRLSTEASLAKTIVCHLGAGASMCAIHQGKSIASTMG 231

Query: 237 FTALDGLPMGTRCGQLDPGVVLYLMQEKKMSAAEITDLLYRESGLKGLSGLSHDMRELEA 296
           FTA+DGLPMGTRCG +DPGV+LYL +   M    +  L+Y+ESG  G+SGLS DM  L  
Sbjct: 232 FTAVDGLPMGTRCGNIDPGVLLYLQRHHHMDTDALEKLIYQESGWLGVSGLSSDMLTLHQ 291

Query: 297 ADTLEAQQAIEYFVFRIRRELGGLAAVLKGIDAIVFCGGIGENSRHVRERVLEGMEWIGV 356
           A T EA++AI+   +RI  ELG L+A ++G++ IVF GG+GEN  ++R+RVL+  +W+G 
Sbjct: 292 AHTPEAEEAIDMLAYRIALELGRLSAAMEGLEQIVFTGGVGENDANLRQRVLKRSQWLGA 351

Query: 357 ELDRSANSANAEVISSERSRTRVFVIPTDEEGMIARHTLALL 398
            +D +AN A+  VI++  S+  + VIPT+EE MIA H   ++
Sbjct: 352 IIDDAANEASLSVINAAASKVVIRVIPTNEEAMIAHHVTEVI 393


Lambda     K      H
   0.322    0.137    0.404 

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: 411
Number of extensions: 12
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: 395
Length adjustment: 31
Effective length of query: 373
Effective length of database: 364
Effective search space:   135772
Effective search space used:   135772
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate WP_054340820.1 Nant_RS06470 (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.679111.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.4e-106  341.8   0.0   2.7e-106  341.6   0.0    1.0  1  NCBI__GCF_001305295.1:WP_054340820.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001305295.1:WP_054340820.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  341.6   0.0  2.7e-106  2.7e-106       4     403 ..       2     392 ..       1     394 [. 0.91

  Alignments for each domain:
  == domain 1  score: 341.6 bits;  conditional E-value: 2.7e-106
                             TIGR00016   4 kkilvlnaGssslkfalldaensekv......llsglve.rikleeariktvedgekkeeeklaiedheeavk 69 
                                           + il +n Gssslk +l+++++ e++      l + l e ri+l+++   +++      +++ + e h++a++
  NCBI__GCF_001305295.1:WP_054340820.1   2 QTILTINGGSSSLKCTLFKTASHEETpiyqfkLGNILGEpRITLSDSSGNKITPPTIDISHVPKNERHKAALR 74 
                                           679****************998777655554444555554678888877778888788888889999****** PP

                             TIGR00016  70 kllntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkv 142
                                           ++ln l++    +  +  +++ GHRvvhGge ft  v++++ ++ +++ +++lAPlH p +l  iea +    
  NCBI__GCF_001305295.1:WP_054340820.1  75 TVLNWLEE----HAPHLRLTAFGHRVVHGGELFTAPVLIDSPTMTALEAFIPLAPLHQPYNLLLIEACQ--AL 141
                                           *******6....45677899*************************************************..56 PP

                             TIGR00016 143 llkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlG 215
                                           +++ ++va+FDt+fH   p     Ya+P+  y++ g+ rYGfHG+s++y+++++ k l  ++   + ivcHlG
  NCBI__GCF_001305295.1:WP_054340820.1 142 KPDLPQVACFDTTFHVGQPAVERHYAIPR-KYTKEGIHRYGFHGLSYEYIQKTL-KRLSTEASLAKTIVCHLG 212
                                           67788***********************5.56778***************8766.5677779999******** PP

                             TIGR00016 216 nGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssD 288
                                            Gas++a+++Gksi  +mG+t ++Gl mGtR+G+iDp+++ yl+ ++ + +d++e+++ ++sG lg+sglssD
  NCBI__GCF_001305295.1:WP_054340820.1 213 AGASMCAIHQGKSIASTMGFTAVDGLPMGTRCGNIDPGVLLYLQRHHHMDTDALEKLIYQESGWLGVSGLSSD 285
                                           ************************************************************************* PP

                             TIGR00016 289 lRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkld 361
                                           + ++ ++      ea+ A++++++Ria  +g+  a++eg l+ ivFtgG+Gen+a++r++vl++ + lG  +d
  NCBI__GCF_001305295.1:WP_054340820.1 286 MLTLHQAH---TPEAEEAIDMLAYRIALELGRLSAAMEG-LEQIVFTGGVGENDANLRQRVLKRSQWLGAIID 354
                                           ****9998...6789**********************99.********************************* PP

                             TIGR00016 362 lelnnaarsgkesvisteeskvkvlviptneelviaeDalrl 403
                                            + n+     + svi+   skv + viptnee +ia+ ++++
  NCBI__GCF_001305295.1:WP_054340820.1 355 DAANE----ASLSVINAAASKVVIRVIPTNEEAMIAHHVTEV 392
                                           **999....66789**********************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (395 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: 21.34
//
[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 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