Alignments for a candidate for ackA in Crocosphaera subtropica ATCC 51142

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Crocosphaera subtropica ATCC 51142

Align Acetate kinase; Acetokinase; EC 2.7.2.1 (characterized)
to candidate WP_024750388.1 CCE_RS24430 acetate kinase

Query= SwissProt::P37877
         (395 letters)



>NCBI__GCF_000017845.1:WP_024750388.1
          Length = 407

 Score =  330 bits (846), Expect = 4e-95
 Identities = 174/395 (44%), Positives = 251/395 (63%), Gaps = 11/395 (2%)

Query: 4   IIAINAGSSSLKFQLF-----EMPSET---VLTKGLVERIGIADSVFTISVNGEKNTEVT 55
           I+ +NAGSSS K  L+     E+P ET   + +  +         VF +  NG K     
Sbjct: 3   ILVLNAGSSSQKSCLYCLDEKELPQETQKPIWSANIDWTATSNQGVFNVKANGIKQHLTL 62

Query: 56  DIPDHAVAVKMLLNKLTE--FGIIKDLNEIDGIGHRVVHGGEKFSDSVLLTDETIKEIED 113
           +  DH   ++ +L+ L +    +I + + I+ +GHRVVHGG  +S++ L+  +    I +
Sbjct: 63  ESNDHHQGIRQMLDTLIQGKTKVIDNFSAINLVGHRVVHGGTNYSEATLINSDVKATITE 122

Query: 114 ISELAPLHNPANIVGIKAFKEVLPNVPAVAVFDTAFHQTMPEQSYLYSLPYEYYEKFGIR 173
           +  LAP HNPA++ GI+  + +L N+P VAVFDTAFH  MP ++  Y +PY++ EK GIR
Sbjct: 123 LIPLAPTHNPAHLEGIEIIESILNNIPQVAVFDTAFHSQMPLENAAYPIPYQWLEK-GIR 181

Query: 174 KYGFHGTSHKYVTERAAELLGRPLKDLRLISCHLGNGASIAAVEGGKSIDTSMGFTPLAG 233
           +YGFHG SH+Y   R AEL+ +PL  L+LI+CHLGNG S+AA++ G SIDT+MGFTPL G
Sbjct: 182 RYGFHGISHQYCANRVAELMNQPLSSLKLITCHLGNGCSLAAIKNGISIDTTMGFTPLEG 241

Query: 234 VAMGTRSGNIDPALIPYIMEKTGQTADEVLNTLNKKSGLLGISGFSSDLRDIVEATKEGN 293
           + MGTR G+IDPA++ Y+M +    A+E+ + LN++SGL GISG SSD+R I +  KEGN
Sbjct: 242 LMMGTRGGSIDPAILIYLMREHNFQAEELNHLLNQESGLKGISGISSDMRAICQGIKEGN 301

Query: 294 ERAETALEVFASRIHKYIGSYAARMSGVDAIIFTAGIGENSVEVRERVLRGLEFMGVYWD 353
           +RA+ A ++F  R+H  +GS    + G+DA++FTAGIGENS  VRE+    L F+G+  D
Sbjct: 302 QRAKLAFDMFIHRLHSCLGSMLTSLGGLDALVFTAGIGENSTIVREKACEALSFLGLELD 361

Query: 354 PALNNVRGEEAFISYPHSPVKVMIIPTDEEVMIAR 388
              NN       IS   S +KV +I T E+  IA+
Sbjct: 362 LFKNNDSPVGVDISSSDSSIKVFVIQTQEDWAIAQ 396


Lambda     K      H
   0.317    0.136    0.381 

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: 373
Number of extensions: 11
Number of successful extensions: 4
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: 395
Length of database: 407
Length adjustment: 31
Effective length of query: 364
Effective length of database: 376
Effective search space:   136864
Effective search space used:   136864
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_024750388.1 CCE_RS24430 (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.1735180.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.9e-153  496.3   0.1   3.2e-153  496.2   0.1    1.0  1  NCBI__GCF_000017845.1:WP_024750388.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000017845.1:WP_024750388.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  496.2   0.1  3.2e-153  3.2e-153       4     404 ..       1     402 [.       1     403 [. 0.96

  Alignments for each domain:
  == domain 1  score: 496.2 bits;  conditional E-value: 3.2e-153
                             TIGR00016   4 kkilvlnaGssslkfalldaen......sekvllsglverikleeariktvedgekkeeeklaiedheeavkk 70 
                                           + ilvlnaGsss+k++l+   +      ++k ++s+ ++++  +++ ++ v+ ++ k++ +l+ +dh++++++
  NCBI__GCF_000017845.1:WP_024750388.1   1 MNILVLNAGSSSQKSCLYCLDEkelpqeTQKPIWSANIDWTATSNQGVFNVKANGIKQHLTLESNDHHQGIRQ 73 
                                           579**************966553465434455***************************************** PP

                             TIGR00016  71 llntlkk.dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkv 142
                                           +l+tl + ++k++++ s i+l+GHRvvhGg++++e+++++++v + i ++++lAP Hnpa+legie++    +
  NCBI__GCF_000017845.1:WP_024750388.1  74 MLDTLIQgKTKVIDNFSAINLVGHRVVHGGTNYSEATLINSDVKATITELIPLAPTHNPAHLEGIEIIE--SI 144
                                           ******99*************************************************************..99 PP

                             TIGR00016 143 llkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlG 215
                                           l++ ++vavFDtafH  +p e++ Y++Py++ + +g+RrYGfHG+sh+y+++r+a+l+n+pl +l+li+cHlG
  NCBI__GCF_000017845.1:WP_024750388.1 145 LNNIPQVAVFDTAFHSQMPLENAAYPIPYQWLE-KGIRRYGFHGISHQYCANRVAELMNQPLSSLKLITCHLG 216
                                           9****************************9986.69************************************* PP

                             TIGR00016 216 nGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssD 288
                                           nG s++a+knG sidt+mG+tPLeGl+mGtR G+iDpai+ yl+ +++  ++e++++ln++sGl gisg+ssD
  NCBI__GCF_000017845.1:WP_024750388.1 217 NGCSLAAIKNGISIDTTMGFTPLEGLMMGTRGGSIDPAILIYLMREHNFQAEELNHLLNQESGLKGISGISSD 289
                                           ************************************************************************* PP

                             TIGR00016 289 lRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkld 361
                                           +R i + ++egn++aklA+++++hR+++++g++++sl g lDa+vFt+GiGen++ vre+++e+l +lGl+ld
  NCBI__GCF_000017845.1:WP_024750388.1 290 MRAICQGIKEGNQRAKLAFDMFIHRLHSCLGSMLTSLGG-LDALVFTAGIGENSTIVREKACEALSFLGLELD 361
                                           *************************************76.********************************* PP

                             TIGR00016 362 lelnnaarsgkesvisteeskvkvlviptneelviaeDalrla 404
                                           l +nn   s     is+++s++kv+vi+t+e+++ia+ +++l 
  NCBI__GCF_000017845.1:WP_024750388.1 362 LFKNN--DSPVGVDISSSDSSIKVFVIQTQEDWAIAQSSWQLY 402
                                           *****..7777888************************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (407 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: 26.62
//
[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