Align pyrroline-5-carboxylate reductase (EC 1.5.1.2) (characterized)
to candidate 202462 SO3354 pyrroline-5-carboxylate reductase (NCBI ptt file)
Query= reanno::PV4:5208627 (272 letters) >FitnessBrowser__MR1:202462 Length = 272 Score = 362 bits (928), Expect = e-105 Identities = 176/272 (64%), Positives = 220/272 (80%) Query: 1 MTQKKICFIGAGNMTRSITSGLVKGGYAPELIHATNPSEGKLIALKQDLGIRVSHDNLQA 60 M+Q+KICFIGAGNMTRSI SGL++ GY + ATNPS+GKL AL D G+RVS DN+ A Sbjct: 1 MSQQKICFIGAGNMTRSIISGLIRSGYPASQVQATNPSQGKLDALATDFGVRVSQDNVSA 60 Query: 61 ADEADVIVLAVKPQLMQQVCEAMSGLNLKDKLIVTIAAGVTAERYHAFFKQPIQLIRTMP 120 A +ADVI+L+VKPQLM+QVC+A+ G+++ +KL++TIAAG+ A RY + QPI LIRTMP Sbjct: 61 AQDADVIILSVKPQLMEQVCQALQGIDMSNKLLITIAAGIKASRYSEYLAQPITLIRTMP 120 Query: 121 NTPTQIGLGMTGLYAEQGVSAQDRELCEQLMQTGGETVWVEKEEDLNQVIALAGSSPAYF 180 NTP QIG+GMTGLYA Q +S + + E+LM +GGE VWV +E D+NQVIALAGSSPAYF Sbjct: 121 NTPMQIGVGMTGLYAPQSLSDAQKAIAERLMSSGGEIVWVNEESDINQVIALAGSSPAYF 180 Query: 181 FLMMEAMIDSAKQDGVDEQTAREMVQQAALGAAAMVKQNPQLSPAQLRENVTSKGGTTAQ 240 FL+ME+MID+ KQ G+DE AR +VQQAALGAA M KQNP+L+ LRENVTSKGGTTAQ Sbjct: 181 FLLMESMIDAGKQMGMDEAKARSLVQQAALGAAMMAKQNPELTLGNLRENVTSKGGTTAQ 240 Query: 241 ALAAFERAGLREIVRTAMHDCMDRAQEMAKQF 272 A+A FE A LR +V+ AM +C++RA+EMAK F Sbjct: 241 AIATFEAADLRGVVKKAMENCINRAEEMAKTF 272 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: 258 Number of extensions: 3 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: 272 Length of database: 272 Length adjustment: 25 Effective length of query: 247 Effective length of database: 247 Effective search space: 61009 Effective search space used: 61009 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 202462 SO3354 (pyrroline-5-carboxylate reductase (NCBI ptt file))
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.26188.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-78 249.7 6.7 2.2e-78 249.5 6.7 1.0 1 lcl|FitnessBrowser__MR1:202462 SO3354 pyrroline-5-carboxylate r Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:202462 SO3354 pyrroline-5-carboxylate reductase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 249.5 6.7 2.2e-78 2.2e-78 1 263 [] 6 268 .. 6 268 .. 0.98 Alignments for each domain: == domain 1 score: 249.5 bits; conditional E-value: 2.2e-78 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPqdleevlael 79 i +iGaGnm ++++sgl+++g + ++++ +++s+ kl+ala+++gv+v++d+++a+++adv++l+vKPq +e+v++ l lcl|FitnessBrowser__MR1:202462 6 ICFIGAGNMTRSIISGLIRSGYP-ASQVQATNPSQGKLDALATDFGVRVSQDNVSAAQDADVIILSVKPQLMEQVCQAL 83 68******************888.8****************************************************** PP TIGR00112 80 kseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelveellkavGkvveve 158 ++ ++ +klli+i+AG+++++++++l++ +++R mPNt+ ++g g+t+++a + s++qk+ +e+l+++ G++v+v+ lcl|FitnessBrowser__MR1:202462 84 QG-IDMSNKLLITIAAGIKASRYSEYLAQPITLIRTMPNTPMQIGVGMTGLYAPQSLSDAQKAIAERLMSSGGEIVWVN 161 **.66699********************99************************************************* PP TIGR00112 159 .eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesge.hpalLkdkVtsPgGtTia 235 e+++++v al+GS+PA++fll+e+++dag ++G+++++a++l++q+ Gaa + +++ e + L+++Vts+gGtT++ lcl|FitnessBrowser__MR1:202462 162 eESDINQVIALAGSSPAYFFLLMESMIDAGKQMGMDEAKARSLVQQAALGAAMMAKQNPElTLGNLRENVTSKGGTTAQ 240 999******************************************************99999***************** PP TIGR00112 236 glavLeekgvrsavieaveaavkrseeL 263 ++a++e++++r+ v +a+e++++r+ee+ lcl|FitnessBrowser__MR1:202462 241 AIATFEAADLRGVVKKAMENCINRAEEM 268 *************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (272 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6.17 // [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