Align pyrroline-5-carboxylate reductase (EC 1.5.1.2) (characterized)
to candidate 6938359 Sama_2478 pyrroline-5-carboxylate reductase (RefSeq)
Query= reanno::PV4:5208627 (272 letters) >FitnessBrowser__SB2B:6938359 Length = 271 Score = 324 bits (831), Expect = 1e-93 Identities = 163/272 (59%), Positives = 209/272 (76%), Gaps = 1/272 (0%) Query: 1 MTQKKICFIGAGNMTRSITSGLVKGGYAPELIHATNPSEGKLIALKQDLGIRVSHDNLQA 60 M KKICFIGAGNM+R+I GL+K GY+ LI ATNPS KL AL D GI S DN+ + Sbjct: 1 MQNKKICFIGAGNMSRAIIGGLIKSGYSASLITATNPSLPKLDALAADYGINTSQDNVPS 60 Query: 61 ADEADVIVLAVKPQLMQQVCEAMSGLNLKDKLIVTIAAGVTAERYHAFFKQPIQLIRTMP 120 A ADVIVL+VKPQLMQ VCE+++G+ + DKL++TIAAG+ RYH +F + ++LIRTMP Sbjct: 61 ASAADVIVLSVKPQLMQAVCESLAGV-VDDKLLITIAAGIPENRYHDYFGKQVKLIRTMP 119 Query: 121 NTPTQIGLGMTGLYAEQGVSAQDRELCEQLMQTGGETVWVEKEEDLNQVIALAGSSPAYF 180 NTP Q+GLGMTGLYA G+ +D+ E LM+ G+ VWV +E +++VIALAGSSPAYF Sbjct: 120 NTPMQLGLGMTGLYAPAGMPDEDKAFAESLMRACGDIVWVNEESGIDKVIALAGSSPAYF 179 Query: 181 FLMMEAMIDSAKQDGVDEQTAREMVQQAALGAAAMVKQNPQLSPAQLRENVTSKGGTTAQ 240 FL +EAMI++ + G+ E AR + QQAA+GAAAMVKQNP L+PA+LR NVTSKGGTTA+ Sbjct: 180 FLFIEAMIEAGVEMGLPEADARTLAQQAAVGAAAMVKQNPGLTPAELRANVTSKGGTTAE 239 Query: 241 ALAAFERAGLREIVRTAMHDCMDRAQEMAKQF 272 A+A FE GLR +V+ AM +C+ RA+EMA+ F Sbjct: 240 AIATFEAGGLRTLVKDAMGNCIKRAEEMARNF 271 Lambda K H 0.317 0.130 0.361 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: 265 Number of extensions: 7 Number of successful extensions: 2 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: 272 Length of database: 271 Length adjustment: 25 Effective length of query: 247 Effective length of database: 246 Effective search space: 60762 Effective search space used: 60762 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: 47 (22.7 bits)
Align candidate 6938359 Sama_2478 (pyrroline-5-carboxylate reductase (RefSeq))
to HMM TIGR00112 (proC: pyrroline-5-carboxylate reductase (EC 1.5.1.2))
# 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.aa/TIGR00112.hmm # target sequence database: /tmp/gapView.13156.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00112 [M=263] Accession: TIGR00112 Description: proC: pyrroline-5-carboxylate reductase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-80 256.1 1.5 2.4e-80 255.9 1.5 1.0 1 lcl|FitnessBrowser__SB2B:6938359 Sama_2478 pyrroline-5-carboxylat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6938359 Sama_2478 pyrroline-5-carboxylate reductase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 255.9 1.5 2.4e-80 2.4e-80 1 263 [] 6 267 .. 6 267 .. 0.97 Alignments for each domain: == domain 1 score: 255.9 bits; conditional E-value: 2.4e-80 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPqdleevla 77 i +iGaGnm +a++ gl+k+g + ++ i +++s +kl+ala+++g+++++d++ +++adv++l+vKPq +++v++ lcl|FitnessBrowser__SB2B:6938359 6 ICFIGAGNMSRAIIGGLIKSGYS-ASLITATNPSLPKLDALAADYGINTSQDNVPSASAADVIVLSVKPQLMQAVCE 81 68*****************9876.7999999999******************************************* PP TIGR00112 78 elkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelveellkavGkv 154 +l++ +klli+i+AG++ ++++++++++ +++R mPNt+ ++g g+t+++a + + +e+k+ +e+l++a+G++ lcl|FitnessBrowser__SB2B:6938359 82 SLAG--VVDDKLLITIAAGIPENRYHDYFGKQVKLIRTMPNTPMQLGLGMTGLYAPAGMPDEDKAFAESLMRACGDI 156 ***9..5679******************************************************************* PP TIGR00112 155 veve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesge.hpalLkdkVtsP 229 v+v+ e+ +d v al+GS+PA++fl+iea+++agv++GLp++ a++la+q+ Gaa++++++ + +pa+L+++Vts+ lcl|FitnessBrowser__SB2B:6938359 157 VWVNeESGIDKVIALAGSSPAYFFLFIEAMIEAGVEMGLPEADARTLAQQAAVGAAAMVKQNPGlTPAELRANVTSK 233 ****8999****************************************************99888************ PP TIGR00112 230 gGtTiaglavLeekgvrsavieaveaavkrseeL 263 gGtT++++a++e++g+r+ v +a+ +++kr+ee+ lcl|FitnessBrowser__SB2B:6938359 234 GGTTAEAIATFEAGGLRTLVKDAMGNCIKRAEEM 267 *******************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (271 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 8.00 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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