Align Galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate PfGW456L13_5042 D-galactarate dehydratase (EC 4.2.1.42)
Query= reanno::WCS417:GFF829 (517 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5042 Length = 517 Score = 1002 bits (2590), Expect = 0.0 Identities = 497/517 (96%), Positives = 507/517 (98%) Query: 1 MQLIEHADSPRSIRLHERDNVVIVVNDQGVPAGTEFPDGLVTVDFIPQSHKVTLEDIPEG 60 MQLIEH+DSPR IRLHERDNVVIVVNDQGVPAGTEF DGLVTVDF+PQSHKVTLEDIPEG Sbjct: 1 MQLIEHSDSPRYIRLHERDNVVIVVNDQGVPAGTEFADGLVTVDFVPQSHKVTLEDIPEG 60 Query: 61 GQIIRYGQTIGYALAPIPRGSWVQEDQLRMPTAPPLDSLPLSTEVPEAQAPLEGFTFEGY 120 GQ+IRYGQ IGYAL PIPRGSWV+EDQLRMPTAPPLDSLPLST+VP AQAPLEGFTFEGY Sbjct: 61 GQVIRYGQVIGYALQPIPRGSWVKEDQLRMPTAPPLDSLPLSTDVPAAQAPLEGFTFEGY 120 Query: 121 RNADGTVGTRNILGITTTVQCVTGVLDHAVKRIKDELLPKYPHVDDVVALTHSYGCGVAI 180 RNADGTVGTRNILGITTTVQCVTGVLDHAVKRIKDELLPKYPHVDDVVALTHSYGCGVAI Sbjct: 121 RNADGTVGTRNILGITTTVQCVTGVLDHAVKRIKDELLPKYPHVDDVVALTHSYGCGVAI 180 Query: 181 TATDAYIPIRTVRNLARNPNLGGEALVISLGCEKLQAGQVMHDNDSSVDLSEPWLYRLQD 240 TATDAYIPIRTVRNLARNPNLGGEALVISLGCEKLQAGQVMH+NDSSVDLSEPWLYRLQD Sbjct: 181 TATDAYIPIRTVRNLARNPNLGGEALVISLGCEKLQAGQVMHENDSSVDLSEPWLYRLQD 240 Query: 241 SSHGFTEMIEQIMALAETRLKKLDQRRRETVPASELILGMQCGGSDAFSGITANPALGYA 300 SSHGFTEMIEQIM LAETRLKKLDQRRRETVPASELILGMQCGGSDAFSGITANPALGYA Sbjct: 241 SSHGFTEMIEQIMELAETRLKKLDQRRRETVPASELILGMQCGGSDAFSGITANPALGYA 300 Query: 301 SDLLLRAGATVMFSEVTEVRDAIYLLTSRAENTQVAQELVREMDWYDRYLAKGEADRSAN 360 SDLLLRAGATVMFSEVTEVRDAIYLLTSRAEN VAQELVREMDWYDRYLAKGEADRSAN Sbjct: 301 SDLLLRAGATVMFSEVTEVRDAIYLLTSRAENQDVAQELVREMDWYDRYLAKGEADRSAN 360 Query: 361 TTPGNKKGGLSNIVEKSLGSIVKSGSSAINGVLGPGERFKGKGLIFCATPASDFVCGTLQ 420 TTPGNKKGGLSNIVEKSLGSIVKSGSSAINGVLGPGERFK KGLIFCATPASDFVCGTLQ Sbjct: 361 TTPGNKKGGLSNIVEKSLGSIVKSGSSAINGVLGPGERFKRKGLIFCATPASDFVCGTLQ 420 Query: 421 LAAGMNLHVFTTGRGTPYGLAMAPVVKVSTRTELAQRWPDLIDIDAGRIATGRATIEELG 480 LAAGMNLHVFTTGRGTPYGLAMAPVVKVSTRTELAQRWPDLIDIDAGRIATGRA+IE+LG Sbjct: 421 LAAGMNLHVFTTGRGTPYGLAMAPVVKVSTRTELAQRWPDLIDIDAGRIATGRASIEDLG 480 Query: 481 WELFHFYLDVASGRKQTWAEHHKLHNDITLFNPAPIT 517 WELFH+YLDVASG+KQTWAE HKLHNDITLFNPAPIT Sbjct: 481 WELFHYYLDVASGKKQTWAEQHKLHNDITLFNPAPIT 517 Lambda K H 0.318 0.135 0.401 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: 985 Number of extensions: 17 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: 517 Length of database: 517 Length adjustment: 35 Effective length of query: 482 Effective length of database: 482 Effective search space: 232324 Effective search space used: 232324 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 (21.7 bits) S2: 52 (24.6 bits)
Align candidate PfGW456L13_5042 (D-galactarate dehydratase (EC 4.2.1.42))
to HMM TIGR03248 (garD: galactarate dehydratase (EC 4.2.1.42))
# 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/TIGR03248.hmm # target sequence database: /tmp/gapView.8110.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03248 [M=507] Accession: TIGR03248 Description: galactar-dH20: galactarate dehydratase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-295 964.4 0.0 6.4e-295 964.2 0.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5042 D-galactarate dehydratase (EC 4. Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5042 D-galactarate dehydratase (EC 4.2.1.42) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 964.2 0.0 6.4e-295 6.4e-295 2 507 .] 12 517 .] 11 517 .] 1.00 Alignments for each domain: == domain 1 score: 964.2 bits; conditional E-value: 6.4e-295 TIGR03248 2 yirvneqdnvaivvndkGlpagtefedgltlvekipqghkvalvdlekgdaiiry 56 yir++e+dnv+ivvnd+G+pagtef+dgl++v+ +pq+hkv+l d+ +g ++iry lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5042 12 YIRLHERDNVVIVVNDQGVPAGTEFADGLVTVDFVPQSHKVTLEDIPEGGQVIRY 66 9****************************************************** PP TIGR03248 57 geviGyavkdiarGswvkeellelpsapaleelplatkvpeklapleGytfeGyr 111 g+viGya++ i+rGswvke++l++p+ap+l++lpl+t vp+++apleG+tfeGyr lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5042 67 GQVIGYALQPIPRGSWVKEDQLRMPTAPPLDSLPLSTDVPAAQAPLEGFTFEGYR 121 ******************************************************* PP TIGR03248 112 nadGsvGtknilgittsvqcvagvvdyavkrikkellpkypnvddvvalnhsyGc 166 nadG+vGt+nilgitt+vqcv+gv+d+avkrik+ellpkyp vddvval+hsyGc lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5042 122 NADGTVGTRNILGITTTVQCVTGVLDHAVKRIKDELLPKYPHVDDVVALTHSYGC 176 ******************************************************* PP TIGR03248 167 GvaidapdaivpirtlrnlalnpnlGGealvvglGceklqperllpeelsavelk 221 Gvai+a+da++pirt+rnla+npnlGGealv++lGceklq+ ++++e+ s+v+l+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5042 177 GVAITATDAYIPIRTVRNLARNPNLGGEALVISLGCEKLQAGQVMHENDSSVDLS 231 ******************************************************* PP TIGR03248 222 daavlrlqdeklGfaemveailelaeerlkklnarkretvpaselvvGlqcGGsd 276 +++++rlqd+++Gf+em+e+i+elae+rlkkl++r+retvpasel++G+qcGGsd lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5042 232 EPWLYRLQDSSHGFTEMIEQIMELAETRLKKLDQRRRETVPASELILGMQCGGSD 286 ******************************************************* PP TIGR03248 277 afsGvtanpavGfaadllvraGatvlfsevtevrdaihlltpraedaevakalir 331 afsG+tanpa+G+a+dll+raGatv+fsevtevrdai+llt+rae+++va+ l+r lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5042 287 AFSGITANPALGYASDLLLRAGATVMFSEVTEVRDAIYLLTSRAENQDVAQELVR 341 ******************************************************* PP TIGR03248 332 emkwydeylarGeadrsanttpGnkkGGlsnivekalGsivksGssaivevlspG 386 em+wyd+yla+GeadrsanttpGnkkGGlsnivek+lGsivksGssai++vl+pG lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5042 342 EMDWYDRYLAKGEADRSANTTPGNKKGGLSNIVEKSLGSIVKSGSSAINGVLGPG 396 ******************************************************* PP TIGR03248 387 ekvkkkGliyaatpasdfvcGtlqlasglnlhvfttGrGtpyGlalvpvikvstr 441 e+ k+kGli++atpasdfvcGtlqla+g+nlhvfttGrGtpyGla++pv+kvstr lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5042 397 ERFKRKGLIFCATPASDFVCGTLQLAAGMNLHVFTTGRGTPYGLAMAPVVKVSTR 451 ******************************************************* PP TIGR03248 442 telaerwadlidldaGriatGeatiedvGwelfrlildvasGrkktwaekyklhn 496 tela+rw dlid+daGriatG+a+ied+Gwelf+ +ldvasG+k+twae++klhn lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5042 452 TELAQRWPDLIDIDAGRIATGRASIEDLGWELFHYYLDVASGKKQTWAEQHKLHN 506 ******************************************************* PP TIGR03248 497 dlalfnpapvt 507 d++lfnpap+t lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5042 507 DITLFNPAPIT 517 **********8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (507 nodes) Target sequences: 1 (517 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 9.96 // [ok]
This GapMind analysis is from Sep 17 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