GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Aquimarina longa SW024

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_062055201.1 N456_RS06675 acetate kinase

Query= BRENDA::Q9WYB1
         (403 letters)



>NCBI__GCF_001401755.1:WP_062055201.1
          Length = 394

 Score =  407 bits (1046), Expect = e-118
 Identities = 216/397 (54%), Positives = 292/397 (73%), Gaps = 11/397 (2%)

Query: 1   MRVLVINSGSSSIKYQLIEMEGEKVLCKGIAERIGIEGSRLVHRVGDEKHVIERE--LPD 58
           M+VLV+NSGSSSIK+QL  M   KV+C G+ ERIG++ +++ ++   E+  IE+E  + +
Sbjct: 1   MQVLVLNSGSSSIKFQLFTMPEAKVICSGMVERIGLDNAKIKYQ--SEQIAIEKEEDIKN 58

Query: 59  HEEALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEVSPL 118
           H++ L+LI N L+D+K+GV++   +I  VGHRVVHGG  F ++V V EEV + I+E+S L
Sbjct: 59  HKDGLQLIANYLMDDKIGVLQSASDISIVGHRVVHGGNTFAKTVEVTEEVKRKIKELSSL 118

Query: 119 APLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRRYGF 178
           APLHNPANL GI  A ++      VAVFDTAFHQTIP +A+ YAIP  + EK+ IR YGF
Sbjct: 119 APLHNPANLEGIIVAEEIFSQANQVAVFDTAFHQTIPVEAHKYAIPNTFLEKHNIRVYGF 178

Query: 179 HGTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGLVMG 238
           HGTSH+YVS++A + LG  +++ KIIT H+GNG S+ AVK GK +D ++GF P+ GL+MG
Sbjct: 179 HGTSHKYVSEKAIDFLG--IQQSKIITIHLGNGCSMTAVKNGKSIDHTLGFAPMNGLIMG 236

Query: 239 TRSGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGDEWC 298
           TR GD+DPAI F+++   G S +E+  +L K+SG+ GL+ G+ SD+RDIE  A KG+  C
Sbjct: 237 TRCGDIDPAILFYMVNTLGYSLEEVNMLLQKESGMLGLT-GY-SDLRDIEAQAEKGNTDC 294

Query: 299 KLVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLDKQK 358
           KL LE+  YRI KYIG+YA  +NG+DAIVFTAG+GENS + R  VC  L+FLG++LD +K
Sbjct: 295 KLALEMNAYRIKKYIGSYATILNGLDAIVFTAGIGENSDLMRSLVCENLDFLGIELDTEK 354

Query: 359 NEETIRGKE-GIISTPDSRVKVLVVPTNEELMIARDT 394
           N   IR KE   IS P SRVKVLV+PTNEEL IA+ +
Sbjct: 355 NR--IRSKETRTISLPSSRVKVLVIPTNEELEIAKQS 389


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: 423
Number of extensions: 11
Number of successful extensions: 5
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: 394
Length adjustment: 31
Effective length of query: 372
Effective length of database: 363
Effective search space:   135036
Effective search space used:   135036
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_062055201.1 N456_RS06675 (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.70555.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.9e-150  485.7   5.6   5.4e-150  485.5   5.6    1.0  1  NCBI__GCF_001401755.1:WP_062055201.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001401755.1:WP_062055201.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  485.5   5.6  5.4e-150  5.4e-150       4     401 ..       1     390 [.       1     394 [] 0.96

  Alignments for each domain:
  == domain 1  score: 485.5 bits;  conditional E-value: 5.4e-150
                             TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 
                                           +++lvln+Gsss+kf+l+ + +  kv++sg+veri l++a+ik  ++++   e++ +i++h+ +++ ++n l+
  NCBI__GCF_001401755.1:WP_062055201.1   1 MQVLVLNSGSSSIKFQLFTMPE-AKVICSGMVERIGLDNAKIK-YQSEQIAIEKEEDIKNHKDGLQLIANYLM 71 
                                           579******************7.6677*************877.455567888999***************** PP

                             TIGR00016  77 k.dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkakn 148
                                           + +  +l++ s+i+++GHRvvhGg++f+++v vt+ev +kik++s+lAPlHnpa+legi  +   ++  +a++
  NCBI__GCF_001401755.1:WP_062055201.1  72 DdKIGVLQSASDISIVGHRVVHGGNTFAKTVEVTEEVKRKIKELSSLAPLHNPANLEGIIVAE--EIFSQANQ 142
                                           867789*****************************************************9999..7778888* PP

                             TIGR00016 149 vavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvs 221
                                           vavFDtafHqtip ea+ Ya+P  + +++++R YGfHGtshkyv+++a + l+   +++++i++HlGnG s++
  NCBI__GCF_001401755.1:WP_062055201.1 143 VAVFDTAFHQTIPVEAHKYAIPNTFLEKHNIRVYGFHGTSHKYVSEKAIDFLGI--QQSKIITIHLGNGCSMT 213
                                           ****************************************************98..9**************** PP

                             TIGR00016 222 avknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdild 294
                                           avknGksid ++G+ P++Gl+mGtR+GdiDpai++y+ +tlg sl+e++ +l+k+sG+lg++g  sDlRdi++
  NCBI__GCF_001401755.1:WP_062055201.1 214 AVKNGKSIDHTLGFAPMNGLIMGTRCGDIDPAILFYMVNTLGYSLEEVNMLLQKESGMLGLTG-YSDLRDIEA 285
                                           ***************************************************************.89******* PP

                             TIGR00016 295 kkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnna 367
                                           + e+gn ++klAl++ ++Ri+kyig+y++ l+g lDaivFt+GiGen+  +r lv+e+l++lG++ld+e+n  
  NCBI__GCF_001401755.1:WP_062055201.1 286 QAEKGNTDCKLALEMNAYRIKKYIGSYATILNG-LDAIVFTAGIGENSDLMRSLVCENLDFLGIELDTEKNR- 356
                                           *******************************88.*************************************9. PP

                             TIGR00016 368 arsgkesvisteeskvkvlviptneelviaeDal 401
                                            rs++ + is + s+vkvlviptneel ia+ ++
  NCBI__GCF_001401755.1:WP_062055201.1 357 IRSKETRTISLPSSRVKVLVIPTNEELEIAKQSF 390
                                           899999************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (394 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 21.04
//
[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:

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:

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:

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:

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