Align glycolaldehyde oxidoreductase large subunit (characterized)
to candidate GFF2054 PGA1_c20870 molybdenum hydroxylase family protein, large subunit
Query= metacyc::MONOMER-18071 (749 letters) >FitnessBrowser__Phaeo:GFF2054 Length = 787 Score = 445 bits (1144), Expect = e-129 Identities = 270/764 (35%), Positives = 418/764 (54%), Gaps = 44/764 (5%) Query: 2 SYVGKPVKRIYDDKFVTGRSTYVDDIRIPA-LYAGFVRSTYPHAIIKRIDVSDALKVNGI 60 S +G KR D +F+TG Y DDI + Y F+RS H + +D SDA + G+ Sbjct: 5 SGIGASPKRREDVRFLTGTGNYTDDINMRGQAYVHFLRSDVAHGRLTSVDTSDAAAMPGV 64 Query: 61 VAVFTAKEINPLLKGGIRPWPTYIDIRSFRYSERKAFP---ENKVKYVGEPVAIVLGQDK 117 V +FT + + GG+ P + R + A P + KV++VG+P+A V+ + Sbjct: 65 VRIFTGADFEGV--GGL-PCGWQVTDRHGEVMQEPAHPVLAQGKVRHVGDPIAAVVAETP 121 Query: 118 YSVRDAIDKVVVEYEPLKPVIRMEEAEKDQVI-IHEELKTNISYKIPF---KAGEVDKAF 173 RDA + +V++ E L VI M+EA KD +H++L +N+ Y F G VDKA Sbjct: 122 EQARDAAEAIVLDIEDLPAVINMKEAVKDGATKVHDDLTSNLCYDWGFVEENRGAVDKAI 181 Query: 174 SESDKVVRVEAINERLIPNPMEPRGIVSRFE--AGTLSIWYSTQVPHYMRSEF-ARILGI 230 ++ V +E +N RL+ NPMEPR V F G +++ ++Q PH +R A +LGI Sbjct: 182 KDAAHVTTLELVNNRLVANPMEPRVAVGDFNRATGDSTLYTTSQNPHVIRLLMGAFVLGI 241 Query: 231 PESKIKVSMPDVGGAFGAKVHLMPEELAVVASSIILGRPVRWTATRSEEMLA-SEARHNV 289 PE K++V PDVGG FG+K+ EE ++ L R V+WT++RSE ++ + R +V Sbjct: 242 PEHKLRVVAPDVGGGFGSKIFHYAEEAFCTFAAKALNRAVKWTSSRSEAFMSDAHGRDHV 301 Query: 290 FTGEVAVKRDGTILGIKGKLLLDLGAYITVTAGIQPLIIP-MMIPGPYKIRNLDIESVAV 348 E+A+ D ++ + ++GAY++ A P + ++ G YK + + AV Sbjct: 302 TKIELALDADNNFTALRTETYANMGAYLSTFAPSVPTWLHGTLMAGNYKTPLIYVNVKAV 361 Query: 349 YTNTPPITMYRGASRPEATYIIERIMSTVADELGLDDVSIREKNLVTELPYTNPFGLRYD 408 +TNT + YRGA RPEATY +ER++ A ELG+D +++R +N +TE PY P + YD Sbjct: 362 FTNTVAVDAYRGAGRPEATYQLERVIDKAARELGVDPIALRRQNFITEFPYATPVAVEYD 421 Query: 409 SGDYVGLLR--EGVKRLGYYELKKWAEEERKKGHRVGVGLAYYLEICSFGP--------- 457 +GDYV + E + L ++ ++ A + KG G+G+ Y+E C P Sbjct: 422 TGDYVATMDKLEEIADLSGFDARRAAS--KAKGKLRGLGVNCYIEACGIAPSNLVGQLGA 479 Query: 458 ----WEYAEVRVDERGDVLVVTGTTPHGQGTETAIAQIVADALQIDISRVRVIWGDTDTV 513 +E A VRV+ G ++V+TG+ HGQG ET+ Q++AD + I V + GDTD Sbjct: 480 RAGLYESATVRVNATGGIVVMTGSHSHGQGHETSFPQVIADMIGIPEDMVEIEHGDTDKA 539 Query: 514 AASMGTYGSRSVTIGGSAAIKVAEKILDKMKRIAASTWNVDVQEVQYEKGEFKLKNDPSK 573 MGTYGSRS+ +GGSA ++ EKI+ K K+IAA +++ + G+F + K Sbjct: 540 PMGMGTYGSRSLAVGGSAMVRATEKIIAKAKKIAAHILEASDADIELKDGQFTVAG-TDK 598 Query: 574 KMSWDDVASIAYRSH-------DPGLVEKIIYE-NDVTFPYGVHIATVEVD-DTGVARVL 624 ++W DV AY H +PGL E Y+ + T+P G + VEVD DTG + Sbjct: 599 SLAWGDVTLAAYVPHNYPLEDIEPGLEETAFYDPANFTYPSGAYACEVEVDPDTGKVTIE 658 Query: 625 EYRAYDDIGKVVNPALAEAQIHGGGVQAVGQALYEQALLNENGQLI-VTYADYYVPTAVE 683 + A DD G +VNP + + Q+HGG Q +GQAL E + +++GQL+ ++ DY +P A + Sbjct: 659 RFAAADDFGNIVNPMIVDGQVHGGIGQGIGQALLEGCVYDDDGQLLSASFMDYAMPRADD 718 Query: 684 APKFTSVFADQYHPSNYPTGSKGVGEAALIVGPAVIIRALEDAI 727 P + + Q ++ P G KG GEA I P ++ A+ DA+ Sbjct: 719 LPFYKVDHSCQTPCTHNPLGVKGCGEAGAIGTPPAVVNAVVDAL 762 Lambda K H 0.317 0.136 0.394 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: 1407 Number of extensions: 73 Number of successful extensions: 11 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: 749 Length of database: 787 Length adjustment: 41 Effective length of query: 708 Effective length of database: 746 Effective search space: 528168 Effective search space used: 528168 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: 55 (25.8 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