GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Caldicellulosiruptor kronotskyensis 2002

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_013430276.1 CALKRO_RS06615 triose-phosphate isomerase

Query= BRENDA::P36204
         (654 letters)



>NCBI__GCF_000166775.1:WP_013430276.1
          Length = 650

 Score =  742 bits (1916), Expect = 0.0
 Identities = 375/651 (57%), Positives = 494/651 (75%), Gaps = 8/651 (1%)

Query: 1   MEKMTIRDVDLKGKRVIMRVDFNVPV-KDGVVQDDTRIRAALPTIKYALEQGAKVILLSH 59
           + K TIRD+D+ GKRV++RVDFNVP  ++G + DD RIR ALPTIKY ++  AKVIL+SH
Sbjct: 4   LNKKTIRDIDVSGKRVLVRVDFNVPQDENGNITDDRRIREALPTIKYLIDHNAKVILVSH 63

Query: 60  LGRPKGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRF 119
           LGRPKG+  P++S+APVAKRLSELLGKEV     V+G++ KK VE++KEG+V+LLEN RF
Sbjct: 64  LGRPKGKFDPKYSMAPVAKRLSELLGKEVVLAKDVIGEDAKKCVEQMKEGDVVLLENVRF 123

Query: 120 HPGETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEIKFLS 179
           H  E +ND E AK  ASLADI+VNDAFGTAHRAHAS  G+A+F+P+VAGFLMEKEI+ L 
Sbjct: 124 HKEEEENDREFAKALASLADIYVNDAFGTAHRAHASTAGVAEFLPAVAGFLMEKEIEMLG 183

Query: 180 KVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVE 239
               NP++P+V +LGGAKVSDKIGVITNL+EK D +LIGGAM +TFLKA G ++G S+ E
Sbjct: 184 NALANPQRPFVAILGGAKVSDKIGVITNLLEKVDSLLIGGAMAYTFLKAKGYKIGKSKCE 243

Query: 240 EDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPE 299
           +DK+D+A+E++ KA+EKGV ++LPV +++A++ +   E   V   D +P+  MG+DIG  
Sbjct: 244 DDKLDVAREIMRKAEEKGVNLLLPVGSIVAKEFKNDTEFMYVP-SDAMPDDMMGMDIGNT 302

Query: 300 TIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIA-ALTEKGAITVVGGGDSAA 358
           TIELF +++  AKT+VWNGPMGVFE  +FA+GT+ +A A+A A+ E GAI ++GGGDSAA
Sbjct: 303 TIELFSKEIKKAKTIVWNGPMGVFEFPNFAKGTEAIARAVAEAVEENGAIAIIGGGDSAA 362

Query: 359 AVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASIADKKKITRKLILAGNWKMHKTISE 418
           AV K G  DK +H+STGGGASLEFLEGK LPGIA + DK    RK I+A NWKM+KT  E
Sbjct: 363 AVEKLGFADKMTHISTGGGASLEFLEGKVLPGIACLLDKN--PRKKIIAANWKMNKTPQE 420

Query: 419 AKKFVSLLVNELHDVKEFEIVVCPPFTALSEVGEILSGRNIKLGAQNVFYEDQGAFTGEI 478
           AK+FV  L   + DV + E+V+C P   +  V E + G NIKLG QN+FYE++GA+TGEI
Sbjct: 421 AKEFVEELKKYIDDV-QAEVVICAPSILVPYVKEAIEGTNIKLGTQNMFYEEKGAYTGEI 479

Query: 479 SPLMLQEIGVEYVIVGHSERRRIFKEDDEFINRKVKAVLEKGMTPILCVGETLEEREKGL 538
           S  ML+ +GVEYV++GHSERR+ F E DE +N+KV A L+ G+ PI+CVGETL++RE G+
Sbjct: 480 SGPMLKAVGVEYVVIGHSERRQYFGETDEIVNKKVLAALKFGIKPIVCVGETLKQREYGV 539

Query: 539 TFCVVEKQVREGFYGLDKEEAKRVVIAYEPVWAIGTGRVATPQQAQEVHAFIRKLLSEMY 598
           T  +V  QV+    G+ KE+ ++VVIAYEP+WAIGTG+ ATP++A  V   IR +++EMY
Sbjct: 540 TDELVRLQVKIALNGVSKEDVEKVVIAYEPIWAIGTGKNATPEEANRVIGVIRNVIAEMY 599

Query: 599 DEETAGSIRILYGGSIKPDNFLGLIVQKDIDGGLVGGASLKESFIELARIM 649
           +E+TA  +RI YGGS+   N   +    +IDGGLVGGASL     E A+I+
Sbjct: 600 NEDTAQKVRIQYGGSVNSANSADIFNMPEIDGGLVGGASLNAQ--EFAKIL 648


Lambda     K      H
   0.317    0.137    0.386 

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: 1140
Number of extensions: 50
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: 654
Length of database: 650
Length adjustment: 38
Effective length of query: 616
Effective length of database: 612
Effective search space:   376992
Effective search space used:   376992
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: 54 (25.4 bits)

Align candidate WP_013430276.1 CALKRO_RS06615 (triose-phosphate isomerase)
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

# 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/TIGR00419.hmm
# target sequence database:        /tmp/gapView.2397592.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00419  [M=228]
Accession:   TIGR00419
Description: tim: triose-phosphate isomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
      9e-62  194.9   3.7    1.9e-61  193.8   3.7    1.5  1  NCBI__GCF_000166775.1:WP_013430276.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166775.1:WP_013430276.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.8   3.7   1.9e-61   1.9e-61       1     227 [.     407     641 ..     407     642 .. 0.96

  Alignments for each domain:
  == domain 1  score: 193.8 bits;  conditional E-value: 1.9e-61
                             TIGR00419   1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGe 72 
                                           ++  n+K+n + ++ ++ v +l++ + +++  ev++  p + ++ vk+++e ++i+++ qn+   ++Ga+tGe
  NCBI__GCF_000166775.1:WP_013430276.1 407 IIAANWKMNKTPQEAKEFVEELKKYIDDVQ-AEVVICAPSILVPYVKEAIEgTNIKLGTQNMFYEEKGAYTGE 478
                                           5889********************998876.67888888899*********99******************** PP

                             TIGR00419  73 isAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaaa 145
                                           is  mlk +G+++v+igHsErR ++ e+de+++kkv  + + g+k++vCvgetl++re + t + v  + ++a
  NCBI__GCF_000166775.1:WP_013430276.1 479 ISGPMLKAVGVEYVVIGHSERRQYFGETDEIVNKKVLAALKFGIKPIVCVGETLKQREYGVTDELVRLQVKIA 551
                                           *************************************************************999999888877 PP

                             TIGR00419 146 A.......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyGasvtaaedaela 210
                                                    e++v+A+EP+++iGtGk +++ ea+ v + +r+ +++  +++ a++vr++yG+sv++a++a+ +
  NCBI__GCF_000166775.1:WP_013430276.1 552 LngvskedVEKVVIAYEPIWAIGTGKNATPEEANRVIGVIRNVIAEmYNEDTAQKVRIQYGGSVNSANSADIF 624
                                           789999999************************************978899********************** PP

                             TIGR00419 211 aqldvdGvLlasavlka 227
                                             +++dG L+++a+l a
  NCBI__GCF_000166775.1:WP_013430276.1 625 NMPEIDGGLVGGASLNA 641
                                           ***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (650 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: 54.80
//
[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