Align ABC transporter for Glycerol, periplasmic substrate-binding component (characterized)
to candidate BPHYT_RS33275 BPHYT_RS33275 ABC transporter substrate-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_796 (577 letters) >FitnessBrowser__BFirm:BPHYT_RS33275 Length = 580 Score = 920 bits (2379), Expect = 0.0 Identities = 436/571 (76%), Positives = 485/571 (84%), Gaps = 1/571 (0%) Query: 7 AIAFAAAALAMGQAAWAGEAEAKKWIDSEFQPSTLNKDQQMAEMKWFIDAAKKLQAKGVK 66 A+A A AA AG EA+KW+DSEFQPSTL+K QQM EMKWFID A L++ GVK Sbjct: 11 AVAGVIATGFTSHAAIAGTPEAQKWVDSEFQPSTLSKQQQMDEMKWFIDTAATLKSAGVK 70 Query: 67 EISVVSETITTHEYESKTLAKAFEEITGIKVKHDLIQEGDVVEKLQTSMQSGKSIYDGWI 126 E+ VVSET+ TH YESKTLAKAF EITGI VKHD+IQEGDVVEKLQTSMQSG+SIYDGWI Sbjct: 71 EVHVVSETLDTHMYESKTLAKAFTEITGISVKHDIIQEGDVVEKLQTSMQSGQSIYDGWI 130 Query: 127 SDSDLIGTHYRYGKIMNLTDYMGGAGKEWTNPGIDLKDYIGTKFTTGPDGKLYQLPDQQF 186 SDSDLIGTHYRYG IM L+DYM G GK++TNPG+D+KD+IGT FTT PD KLYQLPDQQF Sbjct: 131 SDSDLIGTHYRYGVIMPLSDYMTGEGKKYTNPGLDIKDFIGTSFTTAPDKKLYQLPDQQF 190 Query: 187 ANLYWFRADLFDRKDIKDKFKAKYGYDLGVPLNWSAYEDIAEFFTNDVKNIDGKPIYGHM 246 ANLYWFRAD F RKD++DKFKAKYGY+LGVP+NWSAYEDIAEFFTNDVKNIDG+ +YGHM Sbjct: 191 ANLYWFRADWFARKDLQDKFKAKYGYELGVPVNWSAYEDIAEFFTNDVKNIDGEKVYGHM 250 Query: 247 DYGKKDPSLGWRFTDAWLSMAGTADIGAPNGLPIDEWGIRVADDKCTPVGASVARGGATN 306 DYGKKDPSLGWRFTDAWLSMAG AD G PNG+P+DEWG+RV D C VGASV+RGG TN Sbjct: 251 DYGKKDPSLGWRFTDAWLSMAGEADKGIPNGMPVDEWGVRVTPDGCHAVGASVSRGGGTN 310 Query: 307 SPAAVYALTKYVDWMKKYAPKEATGMTFGEAGPVPAQGQIAQQIFWYTAFTADMTKPGLP 366 SPAAV+A TKY+DW+KK+AP EA+GMTF EAGPVPAQG+IAQQIFWY+AFTA M KPG Sbjct: 311 SPAAVFATTKYIDWLKKFAPPEASGMTFNEAGPVPAQGKIAQQIFWYSAFTASMLKPG-N 369 Query: 367 VVNADGTPKWRMAPGPNGPYWKQGMQNGYQDVGSWTFFKDHDANKTAAAWLYAQFVTAKT 426 V NADGTPKWRMAP P+GPYWK GMQNGYQDVGSWTFFK N+ AAAWLYAQFVT+KT Sbjct: 370 VTNADGTPKWRMAPSPHGPYWKDGMQNGYQDVGSWTFFKSTPPNQRAAAWLYAQFVTSKT 429 Query: 427 TSLKKTMVGLTPIRESDIQSKAMTDMAPKLGGLVEFYRSPARVAWSPTGTNVPDYPKLAQ 486 SLKK++ GLT IR+SDI S T A K GGL+EFYRSPARVAW+PTG NVPDYPK+AQ Sbjct: 430 VSLKKSITGLTFIRDSDIHSDYFTKNADKYGGLIEFYRSPARVAWTPTGNNVPDYPKMAQ 489 Query: 487 LWWKNVAQAVTGEKTPQGAMDTLADEMDQVMARLERAGMAHCAPKLNAKSDPNKWLSDKQ 546 LWWKNVA AV GEKTPQ AMD LA EMDQV+ RL+RAGM CAP+LN +S P+KWLSD+ Sbjct: 490 LWWKNVATAVAGEKTPQAAMDNLAKEMDQVLGRLQRAGMKVCAPELNPESSPDKWLSDQH 549 Query: 547 APWKKLANEKPKGETIAYGTLLQAWKDGKTR 577 APWKKLANEKPKGET+ Y LL AWK GK R Sbjct: 550 APWKKLANEKPKGETVKYDQLLTAWKQGKVR 580 Lambda K H 0.315 0.132 0.412 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: 1380 Number of extensions: 65 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: 577 Length of database: 580 Length adjustment: 36 Effective length of query: 541 Effective length of database: 544 Effective search space: 294304 Effective search space used: 294304 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 (21.6 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