Alignments for a candidate for ackA in Pseudovibrio axinellae Ad2

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Pseudovibrio axinellae Ad2

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_068000287.1 PsAD2_RS00020 acetate kinase

Query= BRENDA::Q9WYB1
         (403 letters)



>NCBI__GCF_001623255.1:WP_068000287.1
          Length = 393

 Score =  335 bits (859), Expect = 1e-96
 Identities = 192/404 (47%), Positives = 262/404 (64%), Gaps = 24/404 (5%)

Query: 3   VLVINSGSSSIKYQLIEMEGEKVLCKGIAERIG----IEGSRLVHRVGDEKHVIERELPD 58
           +LV+N+GSSSIK+QL +  GE+ +  G  + +G    I+G      V  ++ +   E  +
Sbjct: 6   ILVLNAGSSSIKFQLFK--GEESVLSGQIDGLGASAWIKGKSAEGDVVMDRALTADEAKN 63

Query: 59  HEEALKLILNTL--VDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEVS 116
           H+ AL++IL  L   D +L       E+DA+GHRVVHG  ++   VLV E+V   +E  +
Sbjct: 64  HDSALQVILELLKKFDPEL-------EVDAIGHRVVHGSSKYSAPVLVTEDVATELESFN 116

Query: 117 PLAPLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRRY 176
            LAPLHNP NL GI  A    PG PNVA FDTAFH+T   K   YA+P +YY++  IRRY
Sbjct: 117 SLAPLHNPHNLAGILGAKAAFPGKPNVACFDTAFHRTQEFKNEAYALPTKYYDE-GIRRY 175

Query: 177 GFHGTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGLV 236
           G HG S  Y+S+    +   ++ + KII  H+GNGAS+ A+++GKCV T+MGFTPL+GL 
Sbjct: 176 GMHGQSFHYISEEMHNV-APEVADGKIIVAHLGNGASMCAIEHGKCVTTTMGFTPLDGLA 234

Query: 237 MGTRSGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGDE 296
           MGTRSG +DP + F++ME++G+S +E+  +LNK+SG+ GLS G S DMRD+EE+      
Sbjct: 235 MGTRSGLIDPGVIFYLMEEKGMSSKEVAHLLNKESGMKGLS-GISQDMRDLEES---DSP 290

Query: 297 WCKLVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLDK 356
                L+ YD R+ + +GA AA M GVDAIVFT G+GENS  TR  +C  LEFLGV++D 
Sbjct: 291 DAARALDYYDNRVKRELGALAAVMGGVDAIVFTGGIGENSSKTRAGICKGLEFLGVEIDA 350

Query: 357 QKNEETIRGKEGI-ISTPDSRVKVLVVPTNEELMIARDTKEIVE 399
             N+   R KE I IS   S+VKV+ +PTNEE MIAR T+ I E
Sbjct: 351 DANK--ARAKEAITISKQSSKVKVMAIPTNEEAMIARQTRVICE 392


Lambda     K      H
   0.318    0.138    0.391 

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: 456
Number of extensions: 27
Number of successful extensions: 8
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: 403
Length of database: 393
Length adjustment: 31
Effective length of query: 372
Effective length of database: 362
Effective search space:   134664
Effective search space used:   134664
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_068000287.1 PsAD2_RS00020 (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.3280787.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.7e-132  425.6   0.1   9.7e-132  425.4   0.1    1.0  1  NCBI__GCF_001623255.1:WP_068000287.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001623255.1:WP_068000287.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  425.4   0.1  9.7e-132  9.7e-132       2     400 ..       2     387 ..       1     392 [. 0.91

  Alignments for each domain:
  == domain 1  score: 425.4 bits;  conditional E-value: 9.7e-132
                             TIGR00016   2 kskkilvlnaGssslkfalldaensekvllsglverikleeariktvedge...kkeeeklaiedheeavkkl 71 
                                           k + ilvlnaGsss+kf+l++ e  e+v lsg ++ +  +  +  +  +g+   ++  +  + ++h++a++ +
  NCBI__GCF_001623255.1:WP_068000287.1   2 KIETILVLNAGSSSIKFQLFKGE--ESV-LSGQIDGLGASAWIKGKSAEGDvvmDRALTADEAKNHDSALQVI 71 
                                           6789****************987..444.899999998877744444444411134445567899******** PP

                             TIGR00016  72 lntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvll 144
                                           l+ lkk     + + e+++iGHRvvhG++k++  v+vt++v  +++ + +lAPlHnp +l gi  ++++   +
  NCBI__GCF_001623255.1:WP_068000287.1  72 LELLKK----FDPELEVDAIGHRVVHGSSKYSAPVLVTEDVATELESFNSLAPLHNPHNLAGILGAKAA--FP 138
                                           **9996....567789**************************************************955..55 PP

                             TIGR00016 145 kaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnG 217
                                            ++nva+FDtafH+t + ++  YalP+++y+e g+RrYG+HG s++y++++++++    ++d ++iv+HlGnG
  NCBI__GCF_001623255.1:WP_068000287.1 139 GKPNVACFDTAFHRTQEFKNEAYALPTKYYDE-GIRRYGMHGQSFHYISEEMHNVAPE-VADGKIIVAHLGNG 209
                                           668***********************999875.9******************998776.9************* PP

                             TIGR00016 218 asvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlR 290
                                           as++a++ Gk++ t+mG+tPL+Gl+mGtRsG iDp++i+yl+e++g+s +e+ ++lnk+sG+ g+sg+s D+R
  NCBI__GCF_001623255.1:WP_068000287.1 210 ASMCAIEHGKCVTTTMGFTPLDGLAMGTRSGLIDPGVIFYLMEEKGMSSKEVAHLLNKESGMKGLSGISQDMR 282
                                           ************************************************************************* PP

                             TIGR00016 291 dildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldle 363
                                           d+++       +a++Al+ y +R+++ +g+ +a + g +DaivFtgGiGen+++ r+ ++++le+lG+++d +
  NCBI__GCF_001623255.1:WP_068000287.1 283 DLEESD---SPDAARALDYYDNRVKRELGALAAVMGG-VDAIVFTGGIGENSSKTRAGICKGLEFLGVEIDAD 351
                                           **9987...6789**********************76.*********************************** PP

                             TIGR00016 364 lnnaarsgkesvisteeskvkvlviptneelviaeDa 400
                                            n+ ar ++   is++ skvkv++iptnee +ia+ +
  NCBI__GCF_001623255.1:WP_068000287.1 352 ANK-ARAKEAITISKQSSKVKVMAIPTNEEAMIARQT 387
                                           **9.9999999***********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (393 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 20.26
//
[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