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.
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:
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