Align 4-hydroxybenzoyl-CoA reductase HbaC subunit (EC 1.3.7.9) (characterized)
to candidate BPHYT_RS10835 BPHYT_RS10835 carbon monoxide dehydrogenase
Query= metacyc::MONOMER-17404 (777 letters) >FitnessBrowser__BFirm:BPHYT_RS10835 Length = 1012 Score = 259 bits (663), Expect = 4e-73 Identities = 239/804 (29%), Positives = 341/804 (42%), Gaps = 55/804 (6%) Query: 24 VTGRARYTADLD-HTGALVARILRSPISHGDIVRLDVSKALALDGVAAIVTGEDCAITYG 82 +TG RY D+ G L A ILRSP +H ++V +D A L GV AI+T +D Sbjct: 42 LTGHGRYGDDIGIRPGTLHAAILRSPHAHAELVSIDTDAASKLPGVHAILTRDDLRAWSR 101 Query: 83 VLPIA----MNEYPMARDRVRYRGEPVAAVAAVDAETARQALDLIELELRELPAYYESEA 138 + M ++ +A DRVRY GEPVA V A A LDL+++E L E Sbjct: 102 PFVVGVKSPMEQWALAMDRVRYVGEPVAVVLAQSRAIAEDGLDLLKVEYATLDPVTSIEQ 161 Query: 139 ARAPDAWLLHDNKPGNIEREVHNEFGDLAAGFEAADLIRTHTHHCAEVNHAQIEPHACLM 198 A + ++ +LH+ N+ + H +G+ A FE A H A IE + Sbjct: 162 AASDESPVLHEKVGSNVISDRHFRYGEPEAAFEKAPHRVKLVAHYPRNTCAPIECGVVIA 221 Query: 199 DYDPVTGRLTAQSVSQVGYYLHLMLARCLEIDPSRVRVIKPF-VGGGFGARVEVLNFEVI 257 +Y S + LH ++A L + +R+R P GG FG + V + V+ Sbjct: 222 EYLAGDEGYDVTSNFMGPFSLHAVMAMALNVPANRLRHKAPRDSGGSFGVKQAVFPYVVL 281 Query: 258 AALLARKASGRVLMRLSREETFITHRARPQTDITLTIGTRRDGRFTACSCEVVQRGGAYA 317 L +RKA V R E + TL DGR TA S + ++ G Y Sbjct: 282 MCLASRKAGAPVKWVEDRFEHLSAATSATARLSTLEAAVESDGRITALSYDQLEDCGGYL 341 Query: 318 GYGIVTILYA-GALLQGLYDIPAVKYDGYRVYTNLPPCGAMRGHGSVDVRHAFENLVDRM 376 Y L G Y I + V TN P G +RG G V A E L+ R+ Sbjct: 342 RAPEPATFYRMHGCLTGAYAIDNLLVRNRVVLTNKTPTGLVRGFGGPQVYFALERLMQRI 401 Query: 377 ARELGLDPFAVRRANLLAA---PTRTLNDLMVNSYGLAECLDKVERASGWHERIGRLPPG 433 A EL LD V R N +AA P R +++S E L + G+ E R Sbjct: 402 ALELKLDVLDVYRRNFVAADAFPYRAAAGALLDSGNYQEALRRALAEGGYDELRARRDAA 461 Query: 434 K------GLGMACSHYVSGSAKPIHFTGEPH-------------AVVALRLDFDGGITAL 474 + G+G A S S T P A + +D GG+ Sbjct: 462 RKEGRLYGIGFAAIVEPSVSNMGYITTVMPAEARKKAGPKSGAIASATVSVDLLGGVVVT 521 Query: 475 TGAADIGQGSSTVVAITVAETLGVALNRVRV-ISGDSAITPKDN-----GAYSSRITFMV 528 + GQG TV A VA+ LGV+ + V V + D T KD G YSSR V Sbjct: 522 IASTPAGQGHMTVCAQVVADVLGVSPHDVVVNVEFD---THKDAWSVAAGNYSSRFAGAV 578 Query: 529 GNAAIDAATKLKQILIAAAARKLEAVPEQIECAGESFFIGSGAQ-AALGFAEVVKAALVD 587 AA +++ + ++++ PE I C E GA+ A F V A Sbjct: 579 AGTVHLAAVRVRDKIARIVSKQMGCAPEDI-CFEEGRIFAKGAEDRAQPFGRVAANAPHW 637 Query: 588 EGAITVKG--------IFTCPPESQGGQHRGGAVGSTMGFSYAAQVVEVSVDDATGLITV 639 A+ +G +F PP + V ++ + +A + V +D ATG + + Sbjct: 638 APALLPEGEEPGLRETVFWNPP-NMAAPDENDRVNTSAAYGFAFDMCGVELDRATGRVRI 696 Query: 640 DKVWAALDCGRAINPLAVVGQVQGAVWMGMGQAMCEETRY-LDGLPAHASFLEYRMPTMI 698 D+ A D G +NP GQ++GA G+G A+ EE RY DG + +Y MPT Sbjct: 697 DRYVTAHDAGTLLNPALADGQIRGAFAQGLGAALMEEFRYGSDGSFQSGTLADYLMPTTC 756 Query: 699 ESPPIEVAIVESVDPFGPFGAKEASEGALAGFPPAMVNAVANAIGIDLDDLPATPDRVVE 758 E P + +E+ PF P GAK EG PP + NAVA+A+G+D LP TP +V+ Sbjct: 757 EVPDPVIVHLETPSPFTPLGAKGLGEGNNMSTPPCIANAVADALGVDDIRLPLTPSKVMA 816 Query: 759 ALA-----RRRREAKRAVAVRAAS 777 + R E + A A + A+ Sbjct: 817 LIGIDDPEPSRPEFREAPAAKPAT 840 Lambda K H 0.320 0.136 0.402 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: 1890 Number of extensions: 98 Number of successful extensions: 9 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: 777 Length of database: 1012 Length adjustment: 43 Effective length of query: 734 Effective length of database: 969 Effective search space: 711246 Effective search space used: 711246 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 (21.8 bits) S2: 56 (26.2 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