Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19); 4-aminobutyrate-pyruvate transaminase (EC 2.6.1.96) (characterized)
to candidate HSERO_RS17580 HSERO_RS17580 hypothetical protein
Query= BRENDA::Q94CE5 (504 letters) >FitnessBrowser__HerbieS:HSERO_RS17580 Length = 440 Score = 245 bits (625), Expect = 3e-69 Identities = 148/433 (34%), Positives = 231/433 (53%), Gaps = 19/433 (4%) Query: 70 PLVIAKSEGSYVYDDTGKKYLDSLAGLWCTALGGNEPRLVSAAVEQLNTLPFYH-SFWNR 128 P+ +A EG + D GK+Y+D+ G + LG PR++ A +Q+ L + H SF+ Sbjct: 14 PMAVA-GEGMELIDQDGKRYIDASGGAAVSCLGHGHPRVIEAIRKQVGELAYAHTSFF-- 70 Query: 129 TTKPSLDLAKVLLEMFTANKMAKAFFTSGGSDANDTQVKLVWYYNNALGRPEKKKFIARK 188 TT P+ +LA +L + + +F SGGS+A + +KL Y +G+P+++ IAR+ Sbjct: 71 TTAPAEELAAMLADA-APGSLNHVYFLSGGSEAVEAALKLARQYYVEVGQPQRRHIIARR 129 Query: 189 KSYHGSTLISASLSGLPPLHQNFDLPAPFVLHTDCPHY-WRFHLPGETEEEFSTRLAKNL 247 +SYHG+TL + ++ G + F +P H P Y +R GE++ ++ RLA L Sbjct: 130 QSYHGNTLGALAIGGNAWRREMF-MPMLIEAHHVSPCYAYRNRADGESDVQYVQRLADEL 188 Query: 248 EDLIIKEGPETIGAFIAEPVMGA-GGVIPPPATYFEKVQAVVKKYDILFIADEVICAFGR 306 E I+ G + + AF+AE V+GA G +PP YF K++AV KY +L I DEV+ GR Sbjct: 189 EQKILSLGADQVIAFVAETVVGATAGAVPPVGDYFRKIRAVCDKYGVLLILDEVMSGMGR 248 Query: 307 LGTMFGCDKYNIKPDLVTLAKALSSAYMPIGAILMSQEVADVINSHSSKLGVFSHGFTYS 366 G +F C++ + PD+V +AK L + Y PIGA++ S + D + S G F HG TY Sbjct: 249 TGYLFACEEDGVVPDIVVIAKGLGAGYQPIGAMICSDHIYDAVLRGS---GFFQHGHTYI 305 Query: 367 GHPVSCAVAIEALKIYKERNIPEYVAKVAPRFQDGVKAFASGSPIIGETRGTGLILGTEF 426 GH +CA A+ K +E + E V + + + ++ +G+ RG GL +G E Sbjct: 306 GHATACAAAVAVQKTIQEERLLENVRQRGEQLRSELRQAFGDQAHVGDIRGRGLFVGVEL 365 Query: 427 VDNKSPNEPFPPEWGVGAFFGAECQKHGMLVRVA--------GDGILMSPPLIISPEEID 478 V +S P P+ A AE K G+LV GD IL++PP I S +I Sbjct: 366 VAERSSKLPLSPDLRTHARVKAEAMKRGLLVYPMGGTIDGKNGDHILLAPPFIASSNDIS 425 Query: 479 ELISIYGKALKAT 491 E++ A+ A+ Sbjct: 426 EIVQRLSDAVAAS 438 Lambda K H 0.318 0.135 0.404 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: 523 Number of extensions: 26 Number of successful extensions: 5 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: 504 Length of database: 440 Length adjustment: 33 Effective length of query: 471 Effective length of database: 407 Effective search space: 191697 Effective search space used: 191697 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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