GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpV in Burkholderia phytofirmans PsJN

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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