Alignments for a candidate for araB in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Alignments for a candidate for araB in Pedobacter sp. GW460-11-11-14-LB5

Align Ribulokinase (EC 2.7.1.16) (characterized)
to candidate CA265_RS08625 CA265_RS08625 ribulokinase

Query= reanno::Pedo557:CA265_RS08625
         (566 letters)



>FitnessBrowser__Pedo557:CA265_RS08625
          Length = 566

 Score = 1151 bits (2977), Expect = 0.0
 Identities = 566/566 (100%), Positives = 566/566 (100%)

Query: 1   MSTANYVIGVDYGTDSVRSVLVDTANGKEIASSVFLYPRWQKGLYCKPAVNQFRQHPLDY 60
           MSTANYVIGVDYGTDSVRSVLVDTANGKEIASSVFLYPRWQKGLYCKPAVNQFRQHPLDY
Sbjct: 1   MSTANYVIGVDYGTDSVRSVLVDTANGKEIASSVFLYPRWQKGLYCKPAVNQFRQHPLDY 60

Query: 61  IEGLTHTIKDCLAKAGGAEIAHLVKGISVDTTGSSPVAVDATGTPLALTKDFEENPNAMF 120
           IEGLTHTIKDCLAKAGGAEIAHLVKGISVDTTGSSPVAVDATGTPLALTKDFEENPNAMF
Sbjct: 61  IEGLTHTIKDCLAKAGGAEIAHLVKGISVDTTGSSPVAVDATGTPLALTKDFEENPNAMF 120

Query: 121 VLWKDHTSVKEAAEINEHATKFDTNYLKYVGGIYSSEWFWSKLLHILRVDLTIKKGAASW 180
           VLWKDHTSVKEAAEINEHATKFDTNYLKYVGGIYSSEWFWSKLLHILRVDLTIKKGAASW
Sbjct: 121 VLWKDHTSVKEAAEINEHATKFDTNYLKYVGGIYSSEWFWSKLLHILRVDLTIKKGAASW 180

Query: 181 VEHCDWIPFLLCGGNDISTMKRSRCAAGHKALWAEEFNGLPPEDFFSSLDPLLAGFRAKL 240
           VEHCDWIPFLLCGGNDISTMKRSRCAAGHKALWAEEFNGLPPEDFFSSLDPLLAGFRAKL
Sbjct: 181 VEHCDWIPFLLCGGNDISTMKRSRCAAGHKALWAEEFNGLPPEDFFSSLDPLLAGFRAKL 240

Query: 241 FTDTYTSDVSAGTLSEEWANKLGLNTDVVVGVGAFDAHMGAVGGQIEPYYLSKVMGTSTC 300
           FTDTYTSDVSAGTLSEEWANKLGLNTDVVVGVGAFDAHMGAVGGQIEPYYLSKVMGTSTC
Sbjct: 241 FTDTYTSDVSAGTLSEEWANKLGLNTDVVVGVGAFDAHMGAVGGQIEPYYLSKVMGTSTC 300

Query: 301 DILVAPNQDLHGKLINGICGQVNGSVIPGMAGLEAGQSAFGDVYAWFKNLISWPLNHLLT 360
           DILVAPNQDLHGKLINGICGQVNGSVIPGMAGLEAGQSAFGDVYAWFKNLISWPLNHLLT
Sbjct: 301 DILVAPNQDLHGKLINGICGQVNGSVIPGMAGLEAGQSAFGDVYAWFKNLISWPLNHLLT 360

Query: 361 ESEVIDEATATALKAELEGKIIANLSKQADALPNEDYAELAIDWLNGRRTPDANQELKGA 420
           ESEVIDEATATALKAELEGKIIANLSKQADALPNEDYAELAIDWLNGRRTPDANQELKGA
Sbjct: 361 ESEVIDEATATALKAELEGKIIANLSKQADALPNEDYAELAIDWLNGRRTPDANQELKGA 420

Query: 421 ITGLGLGTDAPRFFRALAAATCFGAKAIVDRFKEQGVPVKGIIGIGGVAKKSAYIMQMMA 480
           ITGLGLGTDAPRFFRALAAATCFGAKAIVDRFKEQGVPVKGIIGIGGVAKKSAYIMQMMA
Sbjct: 421 ITGLGLGTDAPRFFRALAAATCFGAKAIVDRFKEQGVPVKGIIGIGGVAKKSAYIMQMMA 480

Query: 481 DVLEMPIRIHRFEHTCALGAAMFAAVAAGIYPDIETAMAAMGTGFEKEYKPNIKKQKLYR 540
           DVLEMPIRIHRFEHTCALGAAMFAAVAAGIYPDIETAMAAMGTGFEKEYKPNIKKQKLYR
Sbjct: 481 DVLEMPIRIHRFEHTCALGAAMFAAVAAGIYPDIETAMAAMGTGFEKEYKPNIKKQKLYR 540

Query: 541 QHYQQYLGLGRYLEKYNKKDVKPYLS 566
           QHYQQYLGLGRYLEKYNKKDVKPYLS
Sbjct: 541 QHYQQYLGLGRYLEKYNKKDVKPYLS 566


Lambda     K      H
   0.318    0.135    0.411 

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: 1196
Number of extensions: 27
Number of successful extensions: 1
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: 566
Length of database: 566
Length adjustment: 36
Effective length of query: 530
Effective length of database: 530
Effective search space:   280900
Effective search space used:   280900
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 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate CA265_RS08625 CA265_RS08625 (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.15350.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.8e-182  593.7   0.2   2.1e-182  593.5   0.2    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS08625  CA265_RS08625 ribulokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS08625  CA265_RS08625 ribulokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  593.5   0.2  2.1e-182  2.1e-182       2     535 ..       6     558 ..       5     559 .. 0.94

  Alignments for each domain:
  == domain 1  score: 593.5 bits;  conditional E-value: 2.1e-182
                                  TIGR01234   2 yaiGvdfGtlsgralvvdvatGeelaaavkeyrravvdevldkteaklPadyalqhPadyievleaai 69 
                                                y+iGvd+Gt+s+r+++vd a+G+e+a++v  y+r++++  ++ + +    ++++qhP dyie l  +i
  lcl|FitnessBrowser__Pedo557:CA265_RS08625   6 YVIGVDYGTDSVRSVLVDTANGKEIASSVFLYPRWQKGLYCK-PAV----NQFRQHPLDYIEGLTHTI 68 
                                                9****************************************8.665....9***************** PP

                                  TIGR01234  70 kevlaelgvdp.advv.GiGvdftastivpidsdGnvlallpefaeePhayvklWkdhaaqeeadrin 135
                                                k+ la++g  + a +v Gi vd t+s +v++d+ G++lal ++f+e+P+a+++lWkdh++++ea +in
  lcl|FitnessBrowser__Pedo557:CA265_RS08625  69 KDCLAKAGGAEiAHLVkGISVDTTGSSPVAVDATGTPLALTKDFEENPNAMFVLWKDHTSVKEAAEIN 136
                                                ******98666566555*************************************************** PP

                                  TIGR01234 136 rlaeaeGevflsryg.GlisseWlfakvlqiaeedpeiyeaadrwieaadWivaqlsG.....dlkrs 197
                                                + a +    +l +y+ G++sseW+++k l+i++ d  i + a++w+e +dWi+++l+G      +krs
  lcl|FitnessBrowser__Pedo557:CA265_RS08625 137 EHATKFDTNYL-KYVgGIYSSEWFWSKLLHILRVDLTIKKGAASWVEHCDWIPFLLCGgndisTMKRS 203
                                                *9987655555.5554********************************************9999**** PP

                                  TIGR01234 198 rctaGykalwsesk.gyPsasfleelnPslkrivkdkletdigsvgekaGtltekaakllGlpegvvv 264
                                                rc+aG+kalw e+  g+P+++f+  l+P l+ + + kl+td+++ +++aGtl+e++a++lGl   vvv
  lcl|FitnessBrowser__Pedo557:CA265_RS08625 204 RCAAGHKALWAEEFnGLPPEDFFSSLDPLLAGF-RAKLFTDTYTSDVSAGTLSEEWANKLGLNTDVVV 270
                                                **********988526**************987.689******************************* PP

                                  TIGR01234 265 avgnvdahvsaaaagiaePgklvkiiGtstcdvllgekl....ravkGicGvvdggivpGfiGyeaGq 328
                                                 vg++dah++a++ +  eP  l k++Gtstcd+l++ ++    + ++GicG+v+g+++pG++G+eaGq
  lcl|FitnessBrowser__Pedo557:CA265_RS08625 271 GVGAFDAHMGAVGGQ-IEPYYLSKVMGTSTCDILVAPNQdlhgKLINGICGQVNGSVIPGMAGLEAGQ 337
                                                *************98.8*******************99999999************************ PP

                                  TIGR01234 329 savGdifaWfvkvl.............vppelkeeakek.qlqllealsekaakqesgehglvaldWf 382
                                                sa+Gd++aWf   +             + ++ ++  k++ + ++   ls +a   +  +   +a+dW 
  lcl|FitnessBrowser__Pedo557:CA265_RS08625 338 SAFGDVYAWFKNLIswplnhlltesevIDEATATALKAElEGKIIANLSKQADALPNEDYAELAIDWL 405
                                                **********9988********8888644444444443314468899********************* PP

                                  TIGR01234 383 nGnrsvlvdarlkGvlvgltlatkaeelyralveatafGtrmivetfkesGvaveellaaGGiaeknp 450
                                                nG+r++ ++++lkG ++gl l t+a+  +ral +at fG+++iv+ fke+Gv+v+ ++ +GG+a+k  
  lcl|FitnessBrowser__Pedo557:CA265_RS08625 406 NGRRTPDANQELKGAITGLGLGTDAPRFFRALAAATCFGAKAIVDRFKEQGVPVKGIIGIGGVAKKSA 473
                                                ******************************************************************** PP

                                  TIGR01234 451 lvmqiyadvlnlplkivasdqapalGaaifaavaageyadipkaaakmgsavektltPisenaaryek 518
                                                 +mq++advl++p++i   + ++alGaa+faavaag y di++a a mg+  ek ++P+  + + y +
  lcl|FitnessBrowser__Pedo557:CA265_RS08625 474 YIMQMMADVLEMPIRIHRFEHTCALGAAMFAAVAAGIYPDIETAMAAMGTGFEKEYKPNIKKQKLYRQ 541
                                                ******************************************************************** PP

                                  TIGR01234 519 lyaeykeladyfgkenp 535
                                                 y++y  l  y++k+n+
  lcl|FitnessBrowser__Pedo557:CA265_RS08625 542 HYQQYLGLGRYLEKYNK 558
                                                **************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (536 nodes)
Target sequences:                          1  (566 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: 12.80
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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