Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate 350977 BT1449 biotin carboxylase (NCBI ptt file)
Query= metacyc::MONOMER-13589 (666 letters) >FitnessBrowser__Btheta:350977 Length = 503 Score = 457 bits (1177), Expect = e-133 Identities = 239/480 (49%), Positives = 316/480 (65%), Gaps = 7/480 (1%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSY 60 M KKIL+ANRGEIA R+ +T R M I TVAVY+ DR ALHV A+EA I P + SY Sbjct: 1 MIKKILVANRGEIAMRIFRTCRVMDISTVAVYTHVDRGALHVRYAEEAYCISNSPEDTSY 60 Query: 61 IVIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSK 120 + + I+ K +GA A+HPGYGFLSE DFA E GV+FIGP + I MG K ++ Sbjct: 61 LKPELILAIAKKTGA-AIHPGYGFLSENADFARRCEEEGVIFIGPGADIIAKMGIKTEAR 119 Query: 121 KLAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEG 180 K+ +EAG+ VPG + +E K++ E+GYP+M+KA AGGGGKGMR+ SE E + Sbjct: 120 KIMREAGLPIVPGTETPVQGIEEVKKVAKEVGYPIMLKALAGGGGKGMRLVRSEEEAETA 179 Query: 181 FESSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIE 240 S++EA SFG+D ++IEK++ P HIE+Q++ DK+GN V+L ERECSIQRRNQKVIE Sbjct: 180 LRLSQSEAGTSFGNDAVYIEKYIENPHHIEVQIMGDKYGNVVHLGERECSIQRRNQKVIE 239 Query: 241 EAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT 300 E+PSPF+ + TRK M + A K +GY SAGT+EF++D +NFYFLEMNTRLQVEHPVT Sbjct: 240 ESPSPFVKDETRKKMLKVAVEACKRIGYYSAGTLEFMMDKDQNFYFLEMNTRLQVEHPVT 299 Query: 301 ELITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRLTRYRP 360 E TG+DLV MI VAAG LP++Q D+K +G A+E R+YAEDP NF+PS G +T Sbjct: 300 EECTGVDLVRDMITVAAGNPLPYKQEDIKFSGAAIECRIYAEDPENNFMPSPGVIT---- 355 Query: 361 PVESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTFEVEGI 420 V +R D+ Y G E+S++YDPMIAKLC W TRE+AI M AL +++ GI Sbjct: 356 -VREAPEGRNLRLDSAAYAGFEVSLHYDPMIAKLCCWGRTRESAISNMARALREYKILGI 414 Query: 421 GHNLPFVGAVMDHPRFVKGDITTAFIAEEY-PDGFQGAVLDEPTLRRVAAAAAAMNRVAE 479 +PF V+ + F++G T FI + + + +PT+ +AAA R E Sbjct: 415 KTTIPFHQRVLKNAAFLEGKYDTTFIDTRFDKEDLKRRQNTDPTVAVIAAAVRHYEREKE 474 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: 802 Number of extensions: 30 Number of successful extensions: 4 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