Align mannose-6-phosphate isomerase (EC 5.3.1.8) (characterized)
to candidate BWI76_RS16280 BWI76_RS16280 mannose-6-phosphate isomerase
Query= BRENDA::P25081 (391 letters) >FitnessBrowser__Koxy:BWI76_RS16280 Length = 392 Score = 645 bits (1664), Expect = 0.0 Identities = 325/391 (83%), Positives = 350/391 (89%) Query: 1 MQKLINSVQNYAWGSKTALTELYGIANPQQQPMAELWMGAHPKSSSRITTANGETVSLRD 60 MQKLINSVQNYAWGS TALTELYGIANP PMAELWMGAHPKSSS+I +G SLRD Sbjct: 1 MQKLINSVQNYAWGSHTALTELYGIANPNNLPMAELWMGAHPKSSSQILDNSGTPRSLRD 60 Query: 61 AIEKNKTAMLGEAVANRFGELPFLFKVLCAAQPLSIQVHPNKRNSEIGFAKENAAGIPMD 120 AI+ +K +LGE VA RFGELPFLFKVLCAAQPLSIQVHPNK+ SEIGFAKENAAGIP+D Sbjct: 61 AIDSDKATLLGEKVAGRFGELPFLFKVLCAAQPLSIQVHPNKQASEIGFAKENAAGIPLD 120 Query: 121 AAERNYKDPNHKPELVFALTPFLAMNAFREFSDIVSLLQPVAGAHSAIAHFLQVPNAERL 180 AAERNYKDPNHKPELVFALTPFLAMNAFREFSDIV+LLQPVA AH AIA FL PN E L Sbjct: 121 AAERNYKDPNHKPELVFALTPFLAMNAFREFSDIVNLLQPVADAHPAIAQFLAQPNGEHL 180 Query: 181 SQLFASLLNMQGEEKSRALAVLKAALNSQQGEPWQTIRVISEYYPDDSGLFSPLLLNVVK 240 SQLFASLLNM+GEEK+ AL VL+AAL+S+QGEPWQTIR+I+E+YPDDSGLFSPLLLNVVK Sbjct: 181 SQLFASLLNMKGEEKAHALRVLQAALDSEQGEPWQTIRLIAEFYPDDSGLFSPLLLNVVK 240 Query: 241 LNPGEAMFLFAETPHAYLQGVALEVMANSDNVLRAGLTPKYIDIPELVANVKFEPKPAGE 300 LNPGEAMFLFAETPHAYL+GVALEVMANSDNVLRAGLTPKYIDIPELVANVKF PKPAGE Sbjct: 241 LNPGEAMFLFAETPHAYLRGVALEVMANSDNVLRAGLTPKYIDIPELVANVKFTPKPAGE 300 Query: 301 LLTAPVKSGAELDFPIPVDDFAFSLHDLALQETSIGQHSAAILFCVEGEAVLRKDEQRLV 360 LLT PV GAELDFPIPVDDFAFSLHDL+ Q ++I Q SAAILFCVEGEAV+ KD+ L Sbjct: 301 LLTQPVSRGAELDFPIPVDDFAFSLHDLSAQASTIAQDSAAILFCVEGEAVITKDKHSLT 360 Query: 361 LKPGESAFIGADESPVNASGTGRLARVYNKL 391 LKPGESAFIG +ESPV SG GR+ARV+NKL Sbjct: 361 LKPGESAFIGCNESPVQVSGYGRVARVFNKL 391 Lambda K H 0.317 0.132 0.379 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: 604 Number of extensions: 14 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: 391 Length of database: 392 Length adjustment: 31 Effective length of query: 360 Effective length of database: 361 Effective search space: 129960 Effective search space used: 129960 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: 50 (23.9 bits)
Align candidate BWI76_RS16280 BWI76_RS16280 (mannose-6-phosphate isomerase)
to HMM TIGR00218 (manA: mannose-6-phosphate isomerase, class I (EC 5.3.1.8))
# 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/TIGR00218.hmm # target sequence database: /tmp/gapView.16028.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00218 [M=359] Accession: TIGR00218 Description: manA: mannose-6-phosphate isomerase, class I 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-131 424.8 0.0 1.7e-131 424.6 0.0 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS16280 BWI76_RS16280 mannose-6-phosphat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS16280 BWI76_RS16280 mannose-6-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 424.6 0.0 1.7e-131 1.7e-131 2 354 .. 3 382 .. 1 387 [. 0.97 Alignments for each domain: == domain 1 score: 424.6 bits; conditional E-value: 1.7e-131 TIGR00218 2 kflfrvqknlkerdWGkgtaladllgysipskq.taElWagaHkkgsSkvqng..kkvsLrdliekhksel 69 k++++v ++++WG+ tal++l+g ++p + +aElW+gaH+k+sS+++ + sLrd i+++k +l lcl|FitnessBrowser__Koxy:BWI76_RS16280 3 KLINSV----QNYAWGSHTALTELYGIANPNNLpMAELWMGAHPKSSSQILDNsgTPRSLRDAIDSDKATL 69 345555....559*****************9877****************99656889************* PP TIGR00218 70 lGkaeadrf.elPlLvkvLsaekplsiqvHPdkalakigyake..........krnYkDknhkpelvialt 129 lG+++a rf elP+L+kvL+a++plsiqvHP+k+ ++ig+ake +rnYkD+nhkpelv+alt lcl|FitnessBrowser__Koxy:BWI76_RS16280 70 LGEKVAGRFgELPFLFKVLCAAQPLSIQVHPNKQASEIGFAKEnaagipldaaERNYKDPNHKPELVFALT 140 *********************************************************************** PP TIGR00218 130 dfealkgfkp.......Lkriaelh.........eeaerlgkteawviiasdekikeaaeilkealknske 184 +f+a+++f++ L+++a++h +++e+l++ +a+++++++e++ +a ++l+ al++++ lcl|FitnessBrowser__Koxy:BWI76_RS16280 141 PFLAMNAFREfsdivnlLQPVADAHpaiaqflaqPNGEHLSQLFASLLNMKGEEKAHALRVLQAALDSEQG 211 **********999999999999999********************************************** PP TIGR00218 185 elkekiqrl..iypedvglfkgllLnrvklkpgeaiyvrsgtvHAykggdvlEvmanSdnvvragltdkyl 253 e++++i+++ +yp+d+glf++llLn+vkl+pgea++++++t+HAy++g++lEvmanSdnv+raglt+ky+ lcl|FitnessBrowser__Koxy:BWI76_RS16280 212 EPWQTIRLIaeFYPDDSGLFSPLLLNVVKLNPGEAMFLFAETPHAYLRGVALEVMANSDNVLRAGLTPKYI 282 ******999************************************************************** PP TIGR00218 254 dvkklvevltveekpeeklkeqkqkegaevlflvpieefavlktdlsekaelksqdsalillvleGdglil 324 d+++lv++++++ kp+ +l +q++ +gae++f++p+++fa++ +dls +a+++ qdsa+il+++eG+++i lcl|FitnessBrowser__Koxy:BWI76_RS16280 283 DIPELVANVKFTPKPAGELLTQPVSRGAELDFPIPVDDFAFSLHDLSAQASTIAQDSAAILFCVEGEAVIT 353 *********************************************************************** PP TIGR00218 325 sgekklklkkGesfliaakleevtiegede 354 +++++l lk+Ges++i+ ++++v++ g+ + lcl|FitnessBrowser__Koxy:BWI76_RS16280 354 KDKHSLTLKPGESAFIGCNESPVQVSGY-G 382 **************************98.3 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (359 nodes) Target sequences: 1 (392 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.36 // [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