Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_011840591.1 RSPH17029_RS03905 pyruvate carboxylase
Query= metacyc::MONOMER-13589 (666 letters) >NCBI__GCF_000015985.1:WP_011840591.1 Length = 1154 Score = 388 bits (997), Expect = e-112 Identities = 207/461 (44%), Positives = 293/461 (63%), Gaps = 14/461 (3%) Query: 2 FKKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGP--PPANQS 59 F+KILIANRGEIA RV++ A +MG +TVAVY++ D+ +LH ADEA IG P + Sbjct: 4 FRKILIANRGEIAIRVMRAANEMGKKTVAVYAEEDKLSLHRFKADEAYRIGEGLSPVG-A 62 Query: 60 YIVIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITS 119 Y+ I +I+ + SGA+A+HPGYG LSE DF A +AAG+ FIGP + + A+GDK ++ Sbjct: 63 YLSIPEIIRVAQMSGADAIHPGYGLLSENPDFVEACDAAGIAFIGPKAETMRALGDKASA 122 Query: 120 KKLAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKE 179 +++A AGV +P L D +E + + EIGYP+M+KAS GGGG+GMR SEAE+ + Sbjct: 123 RRVAMAAGVPVIPATEVLGDDMEEIKRQAAEIGYPLMLKASWGGGGRGMRPITSEAELAD 182 Query: 180 GFESSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVI 239 + EA +FG+ ++EK + + RH+E+Q+L DK+G +L+ER+C++QRRNQKV+ Sbjct: 183 KVREGRREAEAAFGNGEGYLEKMIQRARHVEVQILGDKYGAIYHLYERDCTVQRRNQKVV 242 Query: 240 EEAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVD-GQKNFYFLEMNTRLQVEHP 298 E AP+P+L E R + E + V Y AGTVEF++D + FYF+E+N R+QVEH Sbjct: 243 ERAPAPYLTEEQRTEICELGRRICAHVNYECAGTVEFLMDMDSEKFYFIEVNPRVQVEHT 302 Query: 299 VTELITGIDLVEQMIRVAAGEKLPF-----QQSDLKINGWAMESRLYAEDPYRNFLPSIG 353 VTE +TGID+V+ IR+A G L Q D+K++G A++ R+ EDP NF+P G Sbjct: 303 VTEEVTGIDIVQSQIRIAEGATLAEATGCPSQDDIKLSGHALQCRVTTEDPQNNFIPDYG 362 Query: 354 RLTRYRPPVESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALD 413 RLT YR S T + + Y GG I+ YYD ++ K+ WAPT E AI M AL Sbjct: 363 RLTAYR----SATGMGIRLDGGTAYAGGVITRYYDSLLVKVTAWAPTPEKAIARMDRALR 418 Query: 414 TFEVEGIGHNLPFVGAVMDHPRFVKGDITTAFIAEEYPDGF 454 F + G+ N+ FV ++ HP F+ TT FI + PD F Sbjct: 419 EFRIRGVATNIAFVENLLKHPSFLDYSYTTKFI-DTTPDLF 458 Score = 62.8 bits (151), Expect = 9e-14 Identities = 29/64 (45%), Positives = 40/64 (62%) Query: 603 PMPGLVVKINVAEGDEVQEGQALATVEAMKMENILRAERRGTVKKIAAAPGASLRVDDVI 662 PMPG V + V+ G +V+ G L T+EAMKME L A+R TVK + PGA + D++ Sbjct: 1090 PMPGSVASVAVSTGQKVKPGDLLVTIEAMKMETGLHADRAATVKAVHVGPGAQIEAKDLL 1149 Query: 663 MEFE 666 +E E Sbjct: 1150 VELE 1153 Lambda K H 0.318 0.134 0.386 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: 1666 Number of extensions: 64 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 666 Length of database: 1154 Length adjustment: 42 Effective length of query: 624 Effective length of database: 1112 Effective search space: 693888 Effective search space used: 693888 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: 56 (26.2 bits)
This GapMind analysis is from Apr 10 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