Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate 351443 BT1915 pyruvate carboxylase subunit A (NCBI ptt file)
Query= metacyc::MONOMER-13589 (666 letters) >FitnessBrowser__Btheta:351443 Length = 503 Score = 471 bits (1211), Expect = e-137 Identities = 240/490 (48%), Positives = 328/490 (66%), Gaps = 5/490 (1%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSY 60 M KKIL+ANRGEIA RV+++ R+M I ++A++S+ADR A HV ADEA +GP + +SY Sbjct: 1 MIKKILVANRGEIAIRVMRSCREMEITSIAIFSEADRTAKHVLYADEAYCVGPAASKESY 60 Query: 61 IVIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSK 120 + I+KI+E K A+A+HPGYGFLSE FA + ++FIGP +EAMGDKI+++ Sbjct: 61 LNIEKIIEVAKECHADAIHPGYGFLSENATFARRCQEENIIFIGPDPETMEAMGDKISAR 120 Query: 121 KLAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEG 180 EAGV VPG + +EAV++ N+IGYPVM+KAS GGGGKGMR+ S EV+E Sbjct: 121 IKMIEAGVPVVPGTQENLKSVEEAVELCNKIGYPVMLKASMGGGGKGMRLIHSAEEVEEA 180 Query: 181 FESSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIE 240 + ++K+E+ +SFGDD +++EKFV +P HIE Q+L DKHGN ++L ERECS+QRRNQK++E Sbjct: 181 YTTAKSESLSSFGDDTVYLEKFVEEPHHIEFQILGDKHGNVIHLCERECSVQRRNQKIVE 240 Query: 241 EAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT 300 E PS F+ RK MGE+A A AKAV Y AGT+EF+VD +N+YFLEMNTRLQVEHP+T Sbjct: 241 ETPSVFVTPELRKDMGEKAVAAAKAVNYIGAGTIEFLVDKHRNYYFLEMNTRLQVEHPIT 300 Query: 301 ELITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRLTRYRP 360 E + G+DLV++ I+VA G+ L +Q D++ G A+E R+ AED NF+PS G + + Sbjct: 301 EEVVGVDLVKEQIKVADGQVLQLKQKDIQQRGHAIECRICAEDTEMNFMPSPGIIKQITE 360 Query: 361 PVESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTFEVEGI 420 P VR D+ VYEG EI +YYDPMI KL WA RE AIE MR L +++ G+ Sbjct: 361 P-----NGIGVRIDSYVYEGYEIPIYYDPMIGKLIVWATNREYAIERMRRVLHEYKLTGV 415 Query: 421 GHNLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLDEPTLRRVAAAAAAMNRVAEI 480 +N+ ++ A+MD P FV+G T FI + Q + +A AA M+ + + Sbjct: 416 KNNISYLRAIMDTPDFVEGHYDTGFITKNGEHLQQCIMRTSERAENIAMIAAYMDYLMNL 475 Query: 481 RRTRISGTMN 490 R T N Sbjct: 476 EENRGDATDN 485 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: 815 Number of extensions: 33 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: 666 Length of database: 503 Length adjustment: 36 Effective length of query: 630 Effective length of database: 467 Effective search space: 294210 Effective search space used: 294210 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: 53 (25.0 bits)
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