Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate RR42_RS21370 RR42_RS21370 4-aminobutyrate aminotransferase
Query= BRENDA::Q0K2K2 (423 letters) >FitnessBrowser__Cup4G11:RR42_RS21370 Length = 420 Score = 593 bits (1528), Expect = e-174 Identities = 292/419 (69%), Positives = 341/419 (81%), Gaps = 1/419 (0%) Query: 3 MKNLELNQRRTLATPRGVGVMCDFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPR 62 MKN EL +R+ ATPRGVGVMC+F+A+RAEN+ +WDVEG+ Y DFAAGIAVLNTGHRHPR Sbjct: 1 MKNAELVRRKDAATPRGVGVMCNFFAERAENSEIWDVEGKRYIDFAAGIAVLNTGHRHPR 60 Query: 63 VMQAIAAQLERFTHTAYQIVPYQGYVTLAERINALVPIQGLNKTALFTTGAEAVENAIKI 122 +++A+ QLERFTHTAYQIVPY Y+ LAERIN P +G KTA FTTGAEAVENAIKI Sbjct: 61 LVEAMQRQLERFTHTAYQIVPYASYIELAERINQRAPGRGAKKTAFFTTGAEAVENAIKI 120 Query: 123 ARAHTGRPGVIAFSGAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTE 182 ARA TGRPGVIAFSG FHGRT++GMALTGKV PYK+GFGPFP +++HAP+P ALHGVS E Sbjct: 121 ARAATGRPGVIAFSGGFHGRTMMGMALTGKVVPYKVGFGPFPGEVFHAPYPCALHGVSVE 180 Query: 183 RALQALEGLFKTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEV 242 AL+A+E LFK D+DP RVAAII EPVQGEGGF AP F++ LRA+CD+HGI+L+ADEV Sbjct: 181 DALKAMEHLFKADVDPKRVAAIIFEPVQGEGGFNVAPPAFVKALRAICDEHGILLVADEV 240 Query: 243 QTGFGRTGKMFAMSHHDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGN 302 QTGFGRTGK+FAM H+DV PDL TMAKSLAGGMPLSAV GRA +MDAP PGGLGGTYAGN Sbjct: 241 QTGFGRTGKLFAMEHYDVAPDLTTMAKSLAGGMPLSAVCGRAEVMDAPAPGGLGGTYAGN 300 Query: 303 PLAVAAAHAVIDVIEEEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFCD 362 PLAVA+A AV+DV+E E+L R A+LGQ+L L A + P +AE+RGLG+MVA EF Sbjct: 301 PLAVASALAVLDVLEGEQLIPRGAALGQRLVARLEALKARVPQIAEIRGLGAMVAVEF-R 359 Query: 363 PATGQPSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQAL 421 A G P AE + VQ RALE GL+LL+CG YGNVIRFL+PLTI A + L +L L Sbjct: 360 RADGAPDAEFTREVQNRALEQGLLLLSCGVYGNVIRFLFPLTISDAVMNEGLDILADVL 418 Lambda K H 0.321 0.136 0.400 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: 615 Number of extensions: 13 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: 423 Length of database: 420 Length adjustment: 32 Effective length of query: 391 Effective length of database: 388 Effective search space: 151708 Effective search space used: 151708 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 50 (23.9 bits)
Align candidate RR42_RS21370 RR42_RS21370 (4-aminobutyrate aminotransferase)
to HMM TIGR00700 (gabT: 4-aminobutyrate transaminase (EC 2.6.1.19))
# 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/TIGR00700.hmm # target sequence database: /tmp/gapView.17848.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00700 [M=420] Accession: TIGR00700 Description: GABAtrnsam: 4-aminobutyrate transaminase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-195 635.5 1.7 1.8e-195 635.3 1.7 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS21370 RR42_RS21370 4-aminobutyrate ami Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS21370 RR42_RS21370 4-aminobutyrate aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 635.3 1.7 1.8e-195 1.8e-195 2 419 .. 9 419 .. 8 420 .] 0.99 Alignments for each domain: == domain 1 score: 635.3 bits; conditional E-value: 1.8e-195 TIGR00700 2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtaf 70 r++aa+++Gvgv+++++a +ae++e+ dv+G+r+id+aagiavln+Gh+hP++vea++rq+e++thta+ lcl|FitnessBrowser__Cup4G11:RR42_RS21370 9 RKDAATPRGVGVMCNFFAERAENSEIWDVEGKRYIDFAAGIAVLNTGHRHPRLVEAMQRQLERFTHTAY 77 889****************************************************************** PP TIGR00700 71 qvvpyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltma 139 q+vpy sy+elae++n+ aPg g kk++++++Gaeavena+kiar+ tgrpgv+afs+gfhGrt + ma lcl|FitnessBrowser__Cup4G11:RR42_RS21370 78 QIVPYASYIELAERINQRAPGRGAKKTAFFTTGAEAVENAIKIARAATGRPGVIAFSGGFHGRTMMGMA 146 ********************************************************************* PP TIGR00700 140 ltakvkPykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqG 208 lt+kv Pyk+GfGPf++ev++aP+p +++ ++ +d l+a+e+lf+adv++++vaa+++ePvqG lcl|FitnessBrowser__Cup4G11:RR42_RS21370 147 LTGKVVPYKVGFGPFPGEVFHAPYPCALHGVSV------EDALKAMEHLFKADVDPKRVAAIIFEPVQG 209 *****************************9988......66778************************* PP TIGR00700 209 eGGfivpakelvaavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgv 277 eGGf+v++ +v+a++ +c+ehgi+l+adevqtGf rtGklfa+eh+d+ Pdl t+aksla+G+Pls+v lcl|FitnessBrowser__Cup4G11:RR42_RS21370 210 EGGFNVAPPAFVKALRAICDEHGILLVADEVQTGFGRTGKLFAMEHYDVAPDLTTMAKSLAGGMPLSAV 278 ********************************************************************* PP TIGR00700 278 vGraeildapapGglGGtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevpaigdv 346 Grae++dapapGglGGtyaGnPlava+alavld++e e li r +g+++ +l lk+ vp+i+++ lcl|FitnessBrowser__Cup4G11:RR42_RS21370 279 CGRAEVMDAPAPGGLGGTYAGNPLAVASALAVLDVLEGEQLIPRGAALGQRLVARLEALKARVPQIAEI 347 ********************************************************************* PP TIGR00700 347 rglGamiavelvdpdttePdaalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkile 415 rglGam+ave+ +d + Pda +++++++al++Gllll++G++Gn+ir+l Pltisd+ ++egl+il lcl|FitnessBrowser__Cup4G11:RR42_RS21370 348 RGLGAMVAVEFRRAD-GAPDAEFTREVQNRALEQGLLLLSCGVYGNVIRFLFPLTISDAVMNEGLDILA 415 ***********9988.57*************************************************** PP TIGR00700 416 aala 419 ++l+ lcl|FitnessBrowser__Cup4G11:RR42_RS21370 416 DVLT 419 9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (420 nodes) Target sequences: 1 (420 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: 00:00:00.01 # Mc/sec: 11.06 // [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