Alignments for a candidate for ackA in Knoellia flava TL1

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Knoellia flava TL1

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_035948878.1 N798_RS12265 acetate kinase

Query= BRENDA::G4T0C7
         (401 letters)



>NCBI__GCF_000768675.1:WP_035948878.1
          Length = 400

 Score =  372 bits (955), Expect = e-107
 Identities = 199/397 (50%), Positives = 264/397 (66%), Gaps = 14/397 (3%)

Query: 8   ILVINSGSSSIKYRLIALPQEQVLADGLLERIGEQESRIIHRADDSGRLNEIKQSVIAAD 67
           +LV+N+GSSS+KY ++     +  A+G++ERIG    R+ H  D  G   E  Q V   D
Sbjct: 6   VLVVNAGSSSLKYSVLDAESGETAAEGIVERIGGT-GRLKHTRD--GETTE--QEVTCKD 60

Query: 68  HHQAFKAVFEILGEN------CSVDAIGHRVVHGGDRFSGPALVDDDTIASMRALCRIAP 121
           H +A  AV + L E+        + A+GHRVVHGG  F+ P LVDDD + ++ AL  +AP
Sbjct: 61  HAEALDAVRQALREHGPDLATLDLVAVGHRVVHGGPDFTEPVLVDDDVLDAVEALVPLAP 120

Query: 122 LHNPVNLLGIESCLAHFPGVPQVAVFDTAFHQTMPPHAYRYAIPETWYSDYGIRRFGFHG 181
           LHNP NL GI S    FP VPQVAVFDTAFHQ++PP A+ YA+P  W   + +RR+GFHG
Sbjct: 121 LHNPANLEGIRSAREAFPDVPQVAVFDTAFHQSLPPAAHTYAVPREWRERHRVRRYGFHG 180

Query: 182 TSHHYVARRAAEFIGKPFDRSHLITLHLGNGASATAIANGRSVDTSMGFTPLEGLVMGTR 241
           TSH YV+RR A+ +G+  +  +++ LHLGNGASA A+  G SVDTSMG +PLEGLVMGTR
Sbjct: 181 TSHRYVSRRTAQLVGRRPEECNVVVLHLGNGASACAVREGHSVDTSMGLSPLEGLVMGTR 240

Query: 242 SGDLDPAIPLFVEQTENTDTDAIDRALNRESGLKGLCGTNDLRTVLEQTNAGDERARLAL 301
           SGD+DPA+  ++E+    D  A D ALN+ESGL GL G +DLR V  +  AGDE A LA+
Sbjct: 241 SGDVDPALGAYLERVAGLDGTAYDTALNKESGLLGLAGVSDLREVESRREAGDEDAALAV 300

Query: 302 DLYCYRIKKYIGAYYAVLGEVDALVFTGGVGENAAEVRRLACEGLSRLGIAIDEAANSDV 361
           D+  +R++KY+GAY  +LG VDA+ FTGG+GEN++ VR     GL  LG+ +D  AN+  
Sbjct: 301 DVMVHRLRKYVGAYAVLLGRVDAIAFTGGIGENSSLVRAEVVGGLGILGVELDADANA-- 358

Query: 362 TGAIAEIGLA-ESRTRILVIKTDEELQIAREAMAVLD 397
            G    +  A  SR  + V+ TDEEL+IAR  +AVLD
Sbjct: 359 AGEPERLVTAPASRIPVWVVPTDEELEIARACLAVLD 395


Lambda     K      H
   0.320    0.137    0.400 

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: 490
Number of extensions: 16
Number of successful extensions: 3
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: 401
Length of database: 400
Length adjustment: 31
Effective length of query: 370
Effective length of database: 369
Effective search space:   136530
Effective search space used:   136530
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 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate WP_035948878.1 N798_RS12265 (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.3449742.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-141  457.6   0.0   1.9e-141  457.4   0.0    1.0  1  NCBI__GCF_000768675.1:WP_035948878.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000768675.1:WP_035948878.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  457.4   0.0  1.9e-141  1.9e-141       5     402 ..       5     392 ..       1     395 [. 0.95

  Alignments for each domain:
  == domain 1  score: 457.4 bits;  conditional E-value: 1.9e-141
                             TIGR00016   5 kilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkk 77 
                                            +lv+naGssslk+++ldae++e+  ++g+veri   +  +k   dg +++e+++  +dh+ea++++ ++l  
  NCBI__GCF_000768675.1:WP_035948878.1   5 PVLVVNAGSSSLKYSVLDAESGETA-AEGIVERIGGTGR-LKHTRDG-ETTEQEVTCKDHAEALDAVRQALR- 73 
                                           69******************99999.********99988.5555555.677788899***************. PP

                             TIGR00016  78 dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknva 150
                                           ++  +  + ++ ++GHRvvhGg +fte v+v+d+vl++++ +++lAPlHnpa+legi+++   +  +++++va
  NCBI__GCF_000768675.1:WP_035948878.1  74 EHGPDLATLDLVAVGHRVVHGGPDFTEPVLVDDDVLDAVEALVPLAPLHNPANLEGIRSAR--EAFPDVPQVA 144
                                           6877888889999************************************************..8889999*** PP

                             TIGR00016 151 vFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsav 223
                                           vFDtafHq +p  a+ Ya+P+++ +++ vRrYGfHGtsh+yv++r+a+l++++ ++ n++v+HlGnGas +av
  NCBI__GCF_000768675.1:WP_035948878.1 145 VFDTAFHQSLPPAAHTYAVPREWRERHRVRRYGFHGTSHRYVSRRTAQLVGRRPEECNVVVLHLGNGASACAV 217
                                           ************************************************************************* PP

                             TIGR00016 224 knGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkk 296
                                           ++G+s+dtsmGl PLeGlvmGtRsGd+Dpa+  yl+   gl   +  ++lnk+sGllg++g  sDlR+++++ 
  NCBI__GCF_000768675.1:WP_035948878.1 218 REGHSVDTSMGLSPLEGLVMGTRSGDVDPALGAYLERVAGLDGTAYDTALNKESGLLGLAG-VSDLREVESRR 289
                                           *************************************************************.79********* PP

                             TIGR00016 297 eegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaar 369
                                           e+g+e+a+lA++v+vhR++ky+g+y+  l g++Dai FtgGiGen++ vr++v+ +l +lG++ld + n    
  NCBI__GCF_000768675.1:WP_035948878.1 290 EAGDEDAALAVDVMVHRLRKYVGAYAVLL-GRVDAIAFTGGIGENSSLVRAEVVGGLGILGVELDADANA--A 359
                                           *************************9999.77*************************************9..7 PP

                             TIGR00016 370 sgkesvisteeskvkvlviptneelviaeDalr 402
                                            + e++++ + s++ v v+pt+eel ia+ +l 
  NCBI__GCF_000768675.1:WP_035948878.1 360 GEPERLVTAPASRIPVWVVPTDEELEIARACLA 392
                                           78899***********************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (400 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 23.84
//
[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