Alignments for a candidate for araB in Nitriliruptor alkaliphilus DSM 45188

GapMind for catabolism of small carbon sources

Alignments for a candidate for araB in Nitriliruptor alkaliphilus DSM 45188

Align Ribulokinase; EC 2.7.1.16 (characterized)
to candidate WP_052665034.1 NITAL_RS04910 ribulokinase

Query= SwissProt::P94524
         (560 letters)



>NCBI__GCF_000969705.1:WP_052665034.1
          Length = 564

 Score =  556 bits (1434), Expect = e-163
 Identities = 288/558 (51%), Positives = 377/558 (67%), Gaps = 8/558 (1%)

Query: 2   AYTIGVDFGTLSGRAVLVHVQTGEELAAAVKEYRHAVIDTVL-PKTGQKLPRDWALQHPA 60
           A T+GVD+GTLSGRAV+V V+ G+ELA+AV  Y H V+DTVL    G +LP DWALQ   
Sbjct: 6   AVTVGVDYGTLSGRAVVVRVRDGQELASAVHPYPHGVMDTVLIAGDGHRLPPDWALQVAG 65

Query: 61  DYLEVLETTIPSLLEQTGVDPKDIIGIGIDFTACTILPIDSSGQPLCMLPEYEEEPHSYV 120
           DY++VL   +P+ ++  G+DP  +IGIG DFTACT++P  + G PL  LP + + PH+YV
Sbjct: 66  DYVDVLRHAVPAAIDAAGIDPAQVIGIGTDFTACTMVPTTADGTPLSELPAFTDRPHAYV 125

Query: 121 KLWKHHAAQKHADRLNQIAEEEGEAFLQRYGGKISSEWMIPKVMQIAEEAPHIYEAADRI 180
           KLWKHHAAQ  ADR+  +A   GE ++ RYGG ISSEW   K +Q+ EE   +Y+A +  
Sbjct: 126 KLWKHHAAQGQADRITALAHARGEDWISRYGGAISSEWEFAKGLQLLEEDREVYDATEHW 185

Query: 181 IEAADWIVYQLCGSLKRSNCTAGYKAMWSEKAGYPSDDFFEKLNPSMKTITKDKLSGSIH 240
           +EAADWIV+QL G   R+ C+AGYK +  + A YPS  F   L+P        K++  I 
Sbjct: 186 VEAADWIVWQLTGRYVRNACSAGYKGILQDGA-YPSRGFLADLHPDFADFADTKVAHEIG 244

Query: 241 SVGEKAGSLTEKMAKLTGLLPGTAVAVANVDAHVSVPAVGITEPGKMLMIMGTSTCHVLL 300
            +G+ AG LT   A  TGL  G AVAV NVDAHV+  A    EPG+M+ IMGTSTCHV+ 
Sbjct: 245 QLGQLAGRLTADAAAWTGLPEGIAVAVGNVDAHVTAAAANAVEPGQMVAIMGTSTCHVMN 304

Query: 301 GEEVHIVPGMCGVVDNGILPGYAGYEAGQSCVGDHFDWFVKTCVPPAYQEEAKEKNIGVH 360
           G+ +  VPG+CGVVD GIL GY GYEAGQS VGD F W+V   VP +Y   A E+ I +H
Sbjct: 305 GDRLAAVPGICGVVDGGILEGYWGYEAGQSGVGDIFGWYVDHQVPASYATTAAERGISLH 364

Query: 361 ELLSEKANHQAPGESGLLALDWWNGNRSTLVDADLTGMLLGMTLLTKPEEIYRALVEATA 420
           ELL+E A  Q  G  GL+ALDW +GNRS LVD +L+G+L+G +L T+ E++YRAL+EATA
Sbjct: 365 ELLTELAAAQPVGAHGLVALDWHSGNRSVLVDHELSGLLVGASLATRAEDVYRALLEATA 424

Query: 421 YGTRMIIETFKESGVPIEELFAAGGIAEKNPFVMQIYADVTNMDIKISGSPQAPALGSAI 480
           +GTR I+E F+E+GVP+ EL  AGG+  KN F+MQ+YADVT + +    S Q PALGSAI
Sbjct: 425 FGTRTIVEAFREAGVPVTELIVAGGLL-KNRFLMQLYADVTRLPLSTITSDQGPALGSAI 483

Query: 481 FGALAAGKEKGGYDDIKKAAANMGKLKDITYTPNAENAAVYEKLYAEYKELVHYFGK-EN 539
             A+AA    G Y D+++AA +MG+     YTP+ + A  Y+ LYAEY  L  +FG+  N
Sbjct: 484 HAAVAA----GAYRDVREAARSMGRRVVAAYTPDEDAALRYDALYAEYTALHDHFGRGGN 539

Query: 540 HVMKRLKTIKNLQFSSAA 557
            VM+RLK I+    S+ A
Sbjct: 540 DVMRRLKAIRRDALSAPA 557


Lambda     K      H
   0.316    0.133    0.395 

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: 894
Number of extensions: 44
Number of successful extensions: 6
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: 560
Length of database: 564
Length adjustment: 36
Effective length of query: 524
Effective length of database: 528
Effective search space:   276672
Effective search space used:   276672
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: 53 (25.0 bits)

Align candidate WP_052665034.1 NITAL_RS04910 (ribulokinase)
to HMM TIGR01234 (araB: ribulokinase (EC 2.7.1.16))

# 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/TIGR01234.hmm
# target sequence database:        /tmp/gapView.15428.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01234  [M=536]
Accession:   TIGR01234
Description: L-ribulokinase: ribulokinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.4e-241  786.9   5.5   6.3e-241  786.7   5.5    1.0  1  lcl|NCBI__GCF_000969705.1:WP_052665034.1  NITAL_RS04910 ribulokinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000969705.1:WP_052665034.1  NITAL_RS04910 ribulokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  786.7   5.5  6.3e-241  6.3e-241       1     532 [.       6     536 ..       6     541 .. 0.99

  Alignments for each domain:
  == domain 1  score: 786.7 bits;  conditional E-value: 6.3e-241
                                 TIGR01234   1 ayaiGvdfGtlsgralvvdvatGeelaaavkeyrravvdevld.kteaklPadyalqhPadyievleaa 68 
                                               a+++Gvd+Gtlsgra+vv+v +G+ela+av+ y+++v+d+vl    + +lP d+alq+  dy++vl+ a
  lcl|NCBI__GCF_000969705.1:WP_052665034.1   6 AVTVGVDYGTLSGRAVVVRVRDGQELASAVHPYPHGVMDTVLIaGDGHRLPPDWALQVAGDYVDVLRHA 74 
                                               579**************************************9857899********************* PP

                                 TIGR01234  69 ikevlaelgvdpadvvGiGvdftastivpidsdGnvlallpefaeePhayvklWkdhaaqeeadrinrl 137
                                               ++ +++ +g+dpa+v+GiG+dfta+t+vp ++dG++l+ lp f ++PhayvklWk+haaq +adri++l
  lcl|NCBI__GCF_000969705.1:WP_052665034.1  75 VPAAIDAAGIDPAQVIGIGTDFTACTMVPTTADGTPLSELPAFTDRPHAYVKLWKHHAAQGQADRITAL 143
                                               ********************************************************************* PP

                                 TIGR01234 138 aeaeGevflsrygGlisseWlfakvlqiaeedpeiyeaadrwieaadWivaqlsGdlkrsrctaGykal 206
                                               a+a+Ge ++srygG isseW+fak+lq++eed e+y+a ++w+eaadWiv+ql+G+++r+ c+aGyk +
  lcl|NCBI__GCF_000969705.1:WP_052665034.1 144 AHARGEDWISRYGGAISSEWEFAKGLQLLEEDREVYDATEHWVEAADWIVWQLTGRYVRNACSAGYKGI 212
                                               ********************************************************************* PP

                                 TIGR01234 207 wseskgyPsasfleelnPslkrivkdkletdigsvgekaGtltekaakllGlpegvvvavgnvdahvsa 275
                                                ++++ yPs+ fl++l P ++ + + k+ ++ig++g+ aG lt++aa+++Glpeg++vavgnvdahv+a
  lcl|NCBI__GCF_000969705.1:WP_052665034.1 213 LQDGA-YPSRGFLADLHPDFADFADTKVAHEIGQLGQLAGRLTADAAAWTGLPEGIAVAVGNVDAHVTA 280
                                               ****9.*************************************************************** PP

                                 TIGR01234 276 aaagiaePgklvkiiGtstcdvllgeklravkGicGvvdggivpGfiGyeaGqsavGdifaWfvkvlvp 344
                                               aaa++ ePg++v+i+Gtstc+v++g++l av+GicGvvdggi++G++GyeaGqs+vGdif W+v   vp
  lcl|NCBI__GCF_000969705.1:WP_052665034.1 281 AAANAVEPGQMVAIMGTSTCHVMNGDRLAAVPGICGVVDGGILEGYWGYEAGQSGVGDIFGWYVDHQVP 349
                                               ********************************************************************* PP

                                 TIGR01234 345 pelkeeakekqlqllealsekaakqesgehglvaldWfnGnrsvlvdarlkGvlvgltlatkaeelyra 413
                                                 +++ a e++++l+e+l+e+aa q++g hglvaldW++Gnrsvlvd++l+G+lvg +lat ae++yra
  lcl|NCBI__GCF_000969705.1:WP_052665034.1 350 ASYATTAAERGISLHELLTELAAAQPVGAHGLVALDWHSGNRSVLVDHELSGLLVGASLATRAEDVYRA 418
                                               ********************************************************************* PP

                                 TIGR01234 414 lveatafGtrmivetfkesGvaveellaaGGiaeknplvmqiyadvlnlplkivasdqapalGaaifaa 482
                                               l+eatafGtr ive+f+e Gv+v el++aGG+  kn+++mq+yadv+ lpl+ ++sdq palG+ai+aa
  lcl|NCBI__GCF_000969705.1:WP_052665034.1 419 LLEATAFGTRTIVEAFREAGVPVTELIVAGGL-LKNRFLMQLYADVTRLPLSTITSDQGPALGSAIHAA 486
                                               ********************************.9*********************************** PP

                                 TIGR01234 483 vaageyadipkaaakmgsavektltPisenaaryeklyaeykeladyfgk 532
                                               vaag y+d+++aa  mg++v  ++tP  + a ry++lyaey  l+d+fg+
  lcl|NCBI__GCF_000969705.1:WP_052665034.1 487 VAAGAYRDVREAARSMGRRVVAAYTPDEDAALRYDALYAEYTALHDHFGR 536
                                               ************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (536 nodes)
Target sequences:                          1  (564 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 9.76
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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