Alignments for a candidate for araB in Haloglycomyces albus DSM 45210

GapMind for catabolism of small carbon sources

Alignments for a candidate for araB in Haloglycomyces albus DSM 45210

Align ribulokinase (EC 2.7.1.16) (characterized)
to candidate WP_029767220.1 HALAL_RS0102125 ribulokinase

Query= BRENDA::Q9KBQ3
         (563 letters)



>NCBI__GCF_000527155.1:WP_029767220.1
          Length = 550

 Score =  552 bits (1423), Expect = e-161
 Identities = 277/549 (50%), Positives = 378/549 (68%), Gaps = 7/549 (1%)

Query: 3   TKYTIGVDYGTESGRAVLIDLSNGQELADHVTPYRHGVIDQYLPNTNIKLGHEWALQHPL 62
           T+  IG+D+GT SGR +++D + G+ELA     Y+HG I+Q+LP+T+I+LG  WALQ P 
Sbjct: 2   TQAVIGIDFGTLSGRVLVVD-TTGKELASVEQVYKHGSIEQHLPDTDIRLGSSWALQDPD 60

Query: 63  DYVEVLTTSVPAVMKESGVDADDVIGIGVDFTACTMLPVDEEGQPLCLLAQYKDNPHSWV 122
           D+ +VL   VP  +K++G+ A+D++GI  DFTACT+LPV  +G PLC LA+++  PH+W 
Sbjct: 61  DWRDVLRLGVPKALKQAGISANDIVGIATDFTACTVLPVTGDGTPLCELAEFRGRPHAWP 120

Query: 123 KLWKHHAAQDKANAINEMAEKRGEAFLPRYGGKISSEWMIAKVWQILDEAEDVYNRTDQF 182
           KLWKHHAAQD+A+ ++E+A  RGE ++ RYGGKISSEW  AK  QIL+E  ++Y R D++
Sbjct: 121 KLWKHHAAQDQADRVSELAHARGEDWIRRYGGKISSEWEFAKALQILEEDPEIYRRMDRW 180

Query: 183 LEATDWIVSQMTGKIVKNSCTAGYKAIWHKREGYPSNEFFKALDPRLEHLTTTKLRGDIV 242
           +EA DWIV Q+ G   +N CTAGYK   ++   +PS ++  AL P       +KL   + 
Sbjct: 181 IEAADWIVWQLMGSENRNICTAGYKG-QYQDGAWPSKDYLSALHPEFTDFAKSKLEFPLS 239

Query: 243 PLGERAGGLLPEMAEKMGLNPGIAVAVGNVDAHAAVPAVGVTTPGKLVMAMGTSICHMLL 302
           PLG RAGG+    AE  GL  G  VAVGNVDAH    A     PG LV  MGTS CH++ 
Sbjct: 240 PLGSRAGGITTRAAEWTGLRIGTPVAVGNVDAHVTASAAQAVDPGHLVAIMGTSTCHVVN 299

Query: 303 GEKEQEVEGMCGVVEDGIIPGYLGYEAGQSAVGDIFAWFVKHGVSAATFDEAQEKGVNVH 362
            E   EV GMCGVV DGI+PG  G+EAGQS VGDIFAWFVK+GV  +    A+++G+++H
Sbjct: 300 AELLSEVPGMCGVVRDGIVPGLWGFEAGQSGVGDIFAWFVKNGVPDSYTRLAEQRGMSIH 359

Query: 363 ALLEEKASQLRPGESGLLALDWWNGNRSILVDTELSGMLLGYTLQTKPEEIYRALLEATA 422
             L + A++   GE GL+ALDW +GNRSILVD +L+G+L+G +L T+PE+IYRALLE+TA
Sbjct: 360 DYLSKLAAEENVGEHGLIALDWHSGNRSILVDHDLTGVLVGLSLHTRPEQIYRALLESTA 419

Query: 423 FGTRAIVDAFHGRGVEVHELYACGGLPQKNHLLMQIFADVTNREIKVAASKQTPALGAAM 482
           FGTR I+D     GV ++E+   GGL  KN LLMQI+ADV NR + V  S Q PALG+A+
Sbjct: 420 FGTRKIIDTLTTFGVPINEITVAGGL-LKNKLLMQIYADVLNRPLNVLTSTQGPALGSAI 478

Query: 483 FASVAAGSEVGGYDSIEEAAKKMGRVKDETFKPIPEHVAIYEKLYQEYVTLHDYFGRGAN 542
            A+VAA      Y  I+ A+ +MG V+   ++P P++V +Y+ LY EY  LHD+FGR  +
Sbjct: 479 HAAVAADV----YPDIQTASAEMGDVERGVYRPDPDNVTLYDDLYNEYCDLHDHFGRQGS 534

Query: 543 DVMKRLKAL 551
            V+ RL+ +
Sbjct: 535 RVLHRLREI 543


Lambda     K      H
   0.317    0.134    0.402 

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: 886
Number of extensions: 48
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: 563
Length of database: 550
Length adjustment: 36
Effective length of query: 527
Effective length of database: 514
Effective search space:   270878
Effective search space used:   270878
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_029767220.1 HALAL_RS0102125 (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.19800.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.5e-224  731.9   0.0     3e-224  731.6   0.0    1.0  1  lcl|NCBI__GCF_000527155.1:WP_029767220.1  HALAL_RS0102125 ribulokinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000527155.1:WP_029767220.1  HALAL_RS0102125 ribulokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  731.6   0.0    3e-224    3e-224       3     533 ..       5     532 ..       3     535 .. 0.99

  Alignments for each domain:
  == domain 1  score: 731.6 bits;  conditional E-value: 3e-224
                                 TIGR01234   3 aiGvdfGtlsgralvvdvatGeelaaavkeyrravvdevldkteaklPadyalqhPadyievleaaike 71 
                                               +iG+dfGtlsgr lvvd  tG+ela+ ++ y+++ +++ l+ t+ +l + +alq P d+ +vl+  +++
  lcl|NCBI__GCF_000527155.1:WP_029767220.1   5 VIGIDFGTLSGRVLVVDT-TGKELASVEQVYKHGSIEQHLPDTDIRLGSSWALQDPDDWRDVLRLGVPK 72 
                                               8***************95.9************************************************* PP

                                 TIGR01234  72 vlaelgvdpadvvGiGvdftastivpidsdGnvlallpefaeePhayvklWkdhaaqeeadrinrlaea 140
                                               +l+++g+  +d+vGi +dfta+t++p++ dG++l+ l ef  +Pha+ klWk+haaq++adr+++la+a
  lcl|NCBI__GCF_000527155.1:WP_029767220.1  73 ALKQAGISANDIVGIATDFTACTVLPVTGDGTPLCELAEFRGRPHAWPKLWKHHAAQDQADRVSELAHA 141
                                               ********************************************************************* PP

                                 TIGR01234 141 eGevflsrygGlisseWlfakvlqiaeedpeiyeaadrwieaadWivaqlsGdlkrsrctaGykalwse 209
                                               +Ge +++rygG+isseW+fak lqi+eedpeiy+ +drwieaadWiv+ql G+ +r++ctaGyk  +++
  lcl|NCBI__GCF_000527155.1:WP_029767220.1 142 RGEDWIRRYGGKISSEWEFAKALQILEEDPEIYRRMDRWIEAADWIVWQLMGSENRNICTAGYKGQYQD 210
                                               ********************************************************************* PP

                                 TIGR01234 210 skgyPsasfleelnPslkrivkdkletdigsvgekaGtltekaakllGlpegvvvavgnvdahvsaaaa 278
                                               ++ +Ps+++l  l P +  + k+kle ++  +g +aG +t++aa+++Gl  g+ vavgnvdahv+a+aa
  lcl|NCBI__GCF_000527155.1:WP_029767220.1 211 GA-WPSKDYLSALHPEFTDFAKSKLEFPLSPLGSRAGGITTRAAEWTGLRIGTPVAVGNVDAHVTASAA 278
                                               *9.****************************************************************** PP

                                 TIGR01234 279 giaePgklvkiiGtstcdvllgeklravkGicGvvdggivpGfiGyeaGqsavGdifaWfvkvlvppel 347
                                               ++ +Pg+lv+i+Gtstc+v+++e l +v+G+cGvv +givpG++G+eaGqs+vGdifaWfvk+ vp  +
  lcl|NCBI__GCF_000527155.1:WP_029767220.1 279 QAVDPGHLVAIMGTSTCHVVNAELLSEVPGMCGVVRDGIVPGLWGFEAGQSGVGDIFAWFVKNGVPDSY 347
                                               ********************************************************************* PP

                                 TIGR01234 348 keeakekqlqllealsekaakqesgehglvaldWfnGnrsvlvdarlkGvlvgltlatkaeelyralve 416
                                                  a+++++++++ ls +aa++++gehgl+aldW++Gnrs lvd++l+Gvlvgl+l+t +e++yral+e
  lcl|NCBI__GCF_000527155.1:WP_029767220.1 348 TRLAEQRGMSIHDYLSKLAAEENVGEHGLIALDWHSGNRSILVDHDLTGVLVGLSLHTRPEQIYRALLE 416
                                               ********************************************************************* PP

                                 TIGR01234 417 atafGtrmivetfkesGvaveellaaGGiaeknplvmqiyadvlnlplkivasdqapalGaaifaavaa 485
                                               +tafGtr i++t++  Gv+++e+ +aGG+  kn+l+mqiyadvln+pl++ +s+q palG+ai+aavaa
  lcl|NCBI__GCF_000527155.1:WP_029767220.1 417 STAFGTRKIIDTLTTFGVPINEITVAGGL-LKNKLLMQIYADVLNRPLNVLTSTQGPALGSAIHAAVAA 484
                                               *****************************.9************************************** PP

                                 TIGR01234 486 geyadipkaaakmgsavektltPisenaaryeklyaeykeladyfgke 533
                                               ++y di++a+a+mg+     ++P ++n++ y+ ly ey +l+d+fg++
  lcl|NCBI__GCF_000527155.1:WP_029767220.1 485 DVYPDIQTASAEMGDVERGVYRPDPDNVTLYDDLYNEYCDLHDHFGRQ 532
                                               *********************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (536 nodes)
Target sequences:                          1  (550 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: 00:00:00.02
# Mc/sec: 10.96
//
[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