Alignments for a candidate for ackA in Kocuria turfanensis HO-9042

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Kocuria turfanensis HO-9042

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_062735420.1 AYX06_RS08595 acetate kinase

Query= BRENDA::Q9WYB1
         (403 letters)



>NCBI__GCF_001580365.1:WP_062735420.1
          Length = 380

 Score =  343 bits (881), Expect = 4e-99
 Identities = 187/403 (46%), Positives = 257/403 (63%), Gaps = 30/403 (7%)

Query: 1   MRVLVINSGSSSIKYQLIEME----GEKVLCKGIAERIGIEGSRLVHRVGDEKHVIEREL 56
           M VLV+N GSSS+KYQ+ E+E    G  VL  G+ E IG                    +
Sbjct: 1   MLVLVVNCGSSSLKYQVRELEPGADGGTVLTSGLIENIG-----------------SSRI 43

Query: 57  PDHEEALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEVS 116
            DH +AL+L+   L  E  G     + +DA GHRVVHGGERF   VL   E+++ IE + 
Sbjct: 44  QDHTQALELLAGRLETELDG-----RTVDAAGHRVVHGGERFSAPVLATPEIIRDIERLV 98

Query: 117 PLAPLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRRY 176
           PLAPLHNPA ++G++A  K  P +P V VFDTAFH+T+P+  + YA+P  +YE + IRRY
Sbjct: 99  PLAPLHNPAAVLGLRAVQKTWPHLPQVCVFDTAFHRTMPEHVWRYAVPERFYEHWGIRRY 158

Query: 177 GFHGTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGLV 236
           GFHGTSH +V+ +AAE LG   E  + +  H+GNGASV A++ G+  DTSMG+TPL GLV
Sbjct: 159 GFHGTSHDWVTGQAAEFLGIPRERFRAVVAHLGNGASVTAIRDGRSYDTSMGYTPLAGLV 218

Query: 237 MGTRSGDLDPAIPFFIMEKE-GISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGD 295
           MGTR+GDLDP++   ++ ++  ++P+ +  +LNK+SG+  ++     DMR ++EAA +GD
Sbjct: 219 MGTRTGDLDPSVVTAVLRRDPEMTPERLDAVLNKESGLRAVAG--DHDMRAVQEAAERGD 276

Query: 296 EWCKLVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLD 355
           E  +L LE+  YR+AKY+G Y  A+ G  A+VFTAG+GEN+   R+ VC  L  LGV+LD
Sbjct: 277 ERAELALEMAAYRLAKYVGGYHVAVEGAQALVFTAGIGENAAPFRKRVCDRLGALGVRLD 336

Query: 356 KQKNEETIRGKEGIISTPDSRVKVLVVPTNEELMIARDTKEIV 398
              N    RG    IS P S ++VLVVPT+EE  IA  T  +V
Sbjct: 337 DDANAARARGTRR-ISAPGSALEVLVVPTDEEQAIAAATAALV 378


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: 391
Number of extensions: 16
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: 403
Length of database: 380
Length adjustment: 31
Effective length of query: 372
Effective length of database: 349
Effective search space:   129828
Effective search space used:   129828
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_062735420.1 AYX06_RS08595 (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.589961.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.6e-126  408.2   0.0   1.4e-124  401.9   0.0    2.0  1  NCBI__GCF_001580365.1:WP_062735420.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001580365.1:WP_062735420.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  401.9   0.0  1.4e-124  1.4e-124       4     403 ..       1     377 [.       1     379 [. 0.95

  Alignments for each domain:
  == domain 1  score: 401.9 bits;  conditional E-value: 1.4e-124
                             TIGR00016   4 kkilvlnaGssslkfalldaen...sekvllsglverikleeariktvedgekkeeeklaiedheeavkklln 73 
                                           +++lv+n+Gssslk+++ + e    + +vl+sgl+e+i ++                   i+dh++a++ l+ 
  NCBI__GCF_001580365.1:WP_062735420.1   1 MLVLVVNCGSSSLKYQVRELEPgadGGTVLTSGLIENIGSSR------------------IQDHTQALELLAG 55 
                                           579**************9998544478899999999987654..................479********** PP

                             TIGR00016  74 tlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllka 146
                                           +l++      +   +++ GHRvvhGge+f+  v+ t e++++i+++++lAPlHnpa++ g++av+  k+ ++ 
  NCBI__GCF_001580365.1:WP_062735420.1  56 RLET----ELDGRTVDAAGHRVVHGGERFSAPVLATPEIIRDIERLVPLAPLHNPAAVLGLRAVQ--KTWPHL 122
                                           ***8....457889***************************************************..889999 PP

                             TIGR00016 147 knvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGas 219
                                           ++v vFDtafH+t+pe+ + Ya+P+++y++ g+RrYGfHGtsh +vt +aa+ l+ p +  + +v+HlGnGas
  NCBI__GCF_001580365.1:WP_062735420.1 123 PQVCVFDTAFHRTMPEHVWRYAVPERFYEHWGIRRYGFHGTSHDWVTGQAAEFLGIPRERFRAVVAHLGNGAS 195
                                           9************************************************************************ PP

                             TIGR00016 220 vsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisyl.aetlglsldeieetlnkksGllgisglssDlRd 291
                                           v+a+++G+s+dtsmG tPL+GlvmGtR+Gd+Dp++++ +     +++ + +  +lnk+sGl +++g   D+R 
  NCBI__GCF_001580365.1:WP_062735420.1 196 VTAIRDGRSYDTSMGYTPLAGLVMGTRTGDLDPSVVTAVlRRDPEMTPERLDAVLNKESGLRAVAG-DHDMRA 267
                                           ***********************************9876156779*********************.9***** PP

                             TIGR00016 292 ildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlel 364
                                           + ++ e g+e+a+lAl++ ++R+aky+g y  ++eg   a+vFt+GiGenaa  r++v+++l  lG++ld + 
  NCBI__GCF_001580365.1:WP_062735420.1 268 VQEAAERGDERAELALEMAAYRLAKYVGGYHVAVEG-AQALVFTAGIGENAAPFRKRVCDRLGALGVRLDDDA 339
                                           **********************************99.9*********************************** PP

                             TIGR00016 365 nnaarsgkesvisteeskvkvlviptneelviaeDalrl 403
                                           n  ar    + is + s+++vlv+pt+ee +ia  ++ l
  NCBI__GCF_001580365.1:WP_062735420.1 340 NA-ARARGTRRISAPGSALEVLVVPTDEEQAIAAATAAL 377
                                           99.9999999**********************9877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (380 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: 00:00:00.01
# Mc/sec: 12.58
//
[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 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