Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate H281DRAFT_05401 H281DRAFT_05401 Cytochrome c, mono- and diheme variants
Query= reanno::WCS417:GFF2133 (447 letters) >FitnessBrowser__Burk376:H281DRAFT_05401 Length = 431 Score = 439 bits (1128), Expect = e-127 Identities = 212/403 (52%), Positives = 264/403 (65%), Gaps = 6/403 (1%) Query: 41 AGATFEPALVSRGEYVARLSDCVACHSLAGKAPFAGGLEMATPLGAIHATNITPDKSTGI 100 A + + ALV RG Y+A+ DC ACH+ PFAGGL M TP+G I+ TNITPD TGI Sbjct: 28 AASAADQALVQRGAYLAKAGDCAACHTAPKGKPFAGGLPMNTPMGQIYTTNITPDAQTGI 87 Query: 101 GTYSLADFDRAVRHGVAPGGRRLYPAMPYPSYVKLSDDDIKALYAFFMQGIKPANQPNIP 160 G+Y+ DF RA+R GVA G LYPAMPYPSY K++D+D+KALYAFFM G+ P Q N Sbjct: 88 GSYTEQDFARAMREGVAKDGHNLYPAMPYPSYAKVNDEDMKALYAFFMSGVAPVQQANRE 147 Query: 161 SDIPWPLNMRWPIALWNGVFAPTATYAAKPDQDALWNRGAYIVQGPGHCGSCHTPRGLAF 220 SDI WP+NMRWP+ LWN VF Y KP +D WNRGAY++QG GHCGSCHTPRG+AF Sbjct: 148 SDIKWPMNMRWPLKLWNMVFLEKGVYQNKPGKDVAWNRGAYLIQGLGHCGSCHTPRGIAF 207 Query: 221 NEKALDEAGAPFLAGALLDGWYAPSLRQDPNTGLGRWSEPQIVQFLKTGRNAHAVVYGSM 280 EKALDE G+ FL G LLD WYA +L + N GLGRWS+ + FLKTG N HA +GSM Sbjct: 208 QEKALDETGSAFLTGGLLDNWYATNLTGEHNVGLGRWSDQDLQAFLKTGANRHASAFGSM 267 Query: 281 TEAFNNSTQFMQDDDLAAIARYLKSLPGDPQRDGAPWQY--QAVAAVQDAP----GAHTY 334 T NNSTQ + D D+AA+ YLKSLP P++Y Q + P GA Y Sbjct: 268 TSVINNSTQNLNDGDIAAMTTYLKSLPAVGGNGAPPYKYDPQTTKVSLNRPANDAGARVY 327 Query: 335 ATRCASCHGLDGKGQPEWMPPLAGATSALAKESASAINITLNGSQRVVASGVPDAYRMPA 394 C CHG+DG+G + PLAG + L K+++S IN+TLNG++ +V G+P Y MP Sbjct: 328 TAYCMHCHGVDGRGFAPMLAPLAGNPNVLEKDASSLINVTLNGTEDLVIGGIPAPYPMPK 387 Query: 395 FREQLSDTEIAEVLSYVRSTWGNNGGAVDANAVGKLRGHTDPA 437 + L+D +IA+VL++VR+ W N AV A V KLR T A Sbjct: 388 YAPVLNDQQIADVLTFVRAGWNNGAPAVTAADVTKLRKSTQAA 430 Score = 39.3 bits (90), Expect = 2e-07 Identities = 35/128 (27%), Positives = 60/128 (46%), Gaps = 17/128 (13%) Query: 181 APTATYAAKPDQDALWNRGAYIVQGPGHCGSCHT-PRGLAFNEKALDEAGAPFLAGALLD 239 +P + A+ DQ AL RGAY+ + G C +CHT P+G F G P + Sbjct: 23 SPASAAASAADQ-ALVQRGAYLAKA-GDCAACHTAPKGKPF------AGGLPM--NTPMG 72 Query: 240 GWYAPSLRQDPNTGLGRWSEPQIVQFLKTG--RNAHAVVYGSMTEAFNNSTQFMQDDDLA 297 Y ++ D TG+G ++E + ++ G ++ H +Y +M S + D+D+ Sbjct: 73 QIYTTNITPDAQTGIGSYTEQDFARAMREGVAKDGHN-LYPAMPYP---SYAKVNDEDMK 128 Query: 298 AIARYLKS 305 A+ + S Sbjct: 129 ALYAFFMS 136 Lambda K H 0.318 0.133 0.423 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: 639 Number of extensions: 33 Number of successful extensions: 4 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: 447 Length of database: 431 Length adjustment: 32 Effective length of query: 415 Effective length of database: 399 Effective search space: 165585 Effective search space used: 165585 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: 51 (24.3 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