Alignments for a candidate for ackA in Rhizobium grahamii CCGE 502

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Rhizobium grahamii CCGE 502

Align Acetate kinase; EC 2.7.2.1; Acetokinase (uncharacterized)
to candidate WP_016554362.1 RGCCGE502_RS11645 acetate/propionate family kinase

Query= curated2:Q6N143
         (398 letters)



>NCBI__GCF_000298315.2:WP_016554362.1
          Length = 370

 Score =  302 bits (774), Expect = 9e-87
 Identities = 174/398 (43%), Positives = 243/398 (61%), Gaps = 38/398 (9%)

Query: 1   MSDVLLVLNAGSSSIKFALYEAHTEPTADHLICEGGIGSLGHRPHFKVVNSDG-STRYDT 59
           M++ LLVLN GSSS+KF ++E   EP    L+  G +  +G  P  +    +G  TR  T
Sbjct: 1   MNETLLVLNTGSSSLKFQIFE---EPDLTVLM-SGKVTGIGDTPEMRAKLPNGRETR--T 54

Query: 60  YLPEGTSHDDAMAVLIGWIETTFPEHRLSAVGHRVVHGGALFDGPVDVTPEVIAQLRAFD 119
            LP  T HD A++ ++  I       R +AV HRVVHGG  F  PV VTPEV+ +L A  
Sbjct: 55  SLPADTDHDRALSAVMNLIRDHDHAWRTAAVVHRVVHGGQDFAEPVVVTPEVMRRLEALI 114

Query: 120 RLAPLHQPHNVSAIEALAKLHPSLPQIACFDTAFHHRLPEVATAFALPRELTEQGVRRYG 179
            LAPLHQPHN++ I A A+L    P IACFDTAFH    ++A +FALP+++ ++G+RRYG
Sbjct: 115 PLAPLHQPHNLAGITASARLASGAPDIACFDTAFHAGHDKLARSFALPQDMRDKGIRRYG 174

Query: 180 FHGLSYEYIAGRL----PDVAGQAVADGRVVVAHLGAGASMCAMLRCRSIATTMGFTALD 235
           FHGLSYE+I+  L    PD+       GRVV+ HLG GAS+CA+    S+ TTM  TALD
Sbjct: 175 FHGLSYEWISQVLARDYPDLHA-----GRVVIGHLGNGASLCALKAGVSVDTTMSMTALD 229

Query: 236 GLMMGSRCGELDPGVVLYLLEEKSMTAREIEDLLYRESGLLGVSGISDDMRTLLASDDPH 295
           G+ MG+R G +DPG +LY+L +  +    ++D+LY  SGL G+SG+++D+  LL S+DP 
Sbjct: 230 GIPMGTRSGSMDPGAILYMLHDLDLGVETVQDILYERSGLKGLSGLTNDVEALLQSEDPQ 289

Query: 296 ACEAIELFVYRIARELGSLAAALGGLDALVFTGGIGEHASEIRRRVCEQAAWLGVTLDPD 355
           A  A+E F  + A+    +A ++GG+DA+VFTGGIGEHA+ +R  +  +  +LG      
Sbjct: 290 ATFALEYFALKAAQYAAMMAVSMGGIDAVVFTGGIGEHAAPVREAILARLRFLG------ 343

Query: 356 ANASLSGAGRISAPDSKVSAWAIPTDEDLMIARHVWRL 393
                         D KV    IPT+E+ M+A H  +L
Sbjct: 344 --------------DFKVV--VIPTNEERMMATHAKKL 365


Lambda     K      H
   0.321    0.137    0.413 

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: 447
Number of extensions: 18
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: 398
Length of database: 370
Length adjustment: 30
Effective length of query: 368
Effective length of database: 340
Effective search space:   125120
Effective search space used:   125120
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_016554362.1 RGCCGE502_RS11645 (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.3463664.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.8e-99  319.1   0.0    1.4e-97  312.9   0.0    2.0  2  NCBI__GCF_000298315.2:WP_016554362.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000298315.2:WP_016554362.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  312.9   0.0   1.4e-97   1.4e-97       4     357 ..       3     343 ..       1     345 [. 0.95
   2 !    5.0   0.0   0.00044   0.00044     383     403 ..     345     365 ..     343     367 .. 0.87

  Alignments for each domain:
  == domain 1  score: 312.9 bits;  conditional E-value: 1.4e-97
                             TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 
                                           + +lvln+Gssslkf++++  +  +vl+sg v  i     ++ ++ +g ++++   a +dh++a+++++n + 
  NCBI__GCF_000298315.2:WP_016554362.1   3 ETLLVLNTGSSSLKFQIFEEPD-LTVLMSGKVTGIGDTPEMRAKLPNGRETRTSLPADTDHDRALSAVMNLIR 74 
                                           679******************7.8899********999999999****************************9 PP

                             TIGR00016  77 kdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknv 149
                                           +    +++    a++ HRvvhGg++f+e v+vt ev+++++ +++lAPlH p +l gi a         a+++
  NCBI__GCF_000298315.2:WP_016554362.1  75 D----HDHAWRTAAVVHRVVHGGQDFAEPVVVTPEVMRRLEALIPLAPLHQPHNLAGITASA--RLASGAPDI 141
                                           6....45667788999*******************************************999..7778899** PP

                             TIGR00016 150 avFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsa 222
                                           a+FDtafH    + a  +alP + ++++g+RrYGfHG+s+++++q +a+     l+  ++++ HlGnGas++a
  NCBI__GCF_000298315.2:WP_016554362.1 142 ACFDTAFHAGHDKLARSFALP-QDMRDKGIRRYGFHGLSYEWISQVLARDYPD-LHAGRVVIGHLGNGASLCA 212
                                           *********************.667889*******************999987.8999*************** PP

                             TIGR00016 223 vknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildk 295
                                           +k G s+dt+m +t L+G+ mGtRsG++Dp++i y+ + l+l ++ ++++l  +sGl g+sgl++D+  +l+ 
  NCBI__GCF_000298315.2:WP_016554362.1 213 LKAGVSVDTTMSMTALDGIPMGTRSGSMDPGAILYMLHDLDLGVETVQDILYERSGLKGLSGLTNDVEALLQS 285
                                           *******************************************************************999988 PP

                             TIGR00016 296 keegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlG 357
                                               + +a+ Al+ ++ + a+y + ++ s+ g +Da+vFtgGiGe aa vre +l +l++lG
  NCBI__GCF_000298315.2:WP_016554362.1 286 E---DPQATFALEYFALKAAQYAAMMAVSMGG-IDAVVFTGGIGEHAAPVREAILARLRFLG 343
                                           7...7899**********************66.***************************99 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.00044
                             TIGR00016 383 vkvlviptneelviaeDalrl 403
                                           +kv+viptnee ++a  a +l
  NCBI__GCF_000298315.2:WP_016554362.1 345 FKVVVIPTNEERMMATHAKKL 365
                                           79*************998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (370 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: 00:00:00.01
# Mc/sec: 10.61
//
[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