GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpV in Cupriavidus basilensis 4G11

Align ABC transporter for Glycerol, periplasmic substrate-binding component (characterized)
to candidate RR42_RS13765 RR42_RS13765 ABC transporter substrate-binding protein

Query= reanno::acidovorax_3H11:Ac3H11_796
         (577 letters)



>FitnessBrowser__Cup4G11:RR42_RS13765
          Length = 576

 Score = 1007 bits (2604), Expect = 0.0
 Identities = 475/577 (82%), Positives = 517/577 (89%), Gaps = 1/577 (0%)

Query: 1   MKMQFKAIAFAAAALAMGQAAWAGEAEAKKWIDSEFQPSTLNKDQQMAEMKWFIDAAKKL 60
           MK+   A+A  AAALA G AAWAGEAEAKKW+DSEFQPS+L KD+Q+AEMKWF+DAA KL
Sbjct: 1   MKLGMTALA-CAAALACGHAAWAGEAEAKKWVDSEFQPSSLAKDKQLAEMKWFMDAAAKL 59

Query: 61  QAKGVKEISVVSETITTHEYESKTLAKAFEEITGIKVKHDLIQEGDVVEKLQTSMQSGKS 120
           +AKGV +ISVVSET+TTHEYESKTLAKAFEEITGIKV HD+IQEGDVVEKLQTSMQSGKS
Sbjct: 60  KAKGVTQISVVSETLTTHEYESKTLAKAFEEITGIKVNHDIIQEGDVVEKLQTSMQSGKS 119

Query: 121 IYDGWISDSDLIGTHYRYGKIMNLTDYMGGAGKEWTNPGIDLKDYIGTKFTTGPDGKLYQ 180
           IYDGWISDSDLIGTHYRYG I+ L+DYM GAGKEWTNPG+D+KD+IGTKFTT PDGKLYQ
Sbjct: 120 IYDGWISDSDLIGTHYRYGAILPLSDYMSGAGKEWTNPGLDVKDFIGTKFTTAPDGKLYQ 179

Query: 181 LPDQQFANLYWFRADLFDRKDIKDKFKAKYGYDLGVPLNWSAYEDIAEFFTNDVKNIDGK 240
           LPDQQFANLYWFRAD F RKD++DKFKAKYGYDLGVP NWSAYEDIA FF+NDVK +DGK
Sbjct: 180 LPDQQFANLYWFRADWFARKDLQDKFKAKYGYDLGVPTNWSAYEDIANFFSNDVKELDGK 239

Query: 241 PIYGHMDYGKKDPSLGWRFTDAWLSMAGTADIGAPNGLPIDEWGIRVADDKCTPVGASVA 300
            +YGHMDYGKKDPSLGWRFTDAWLSMAG AD G PNG+P+DEWGIRV  DKCTP GASVA
Sbjct: 240 KVYGHMDYGKKDPSLGWRFTDAWLSMAGAADKGLPNGMPVDEWGIRVGADKCTPEGASVA 299

Query: 301 RGGATNSPAAVYALTKYVDWMKKYAPKEATGMTFGEAGPVPAQGQIAQQIFWYTAFTADM 360
           RGGA NSPAAVYALTKY+DWMKKYAP +A GMTF EAGPVPAQGQIAQQ+FWYTAFTADM
Sbjct: 300 RGGAANSPAAVYALTKYIDWMKKYAPPQAMGMTFSEAGPVPAQGQIAQQVFWYTAFTADM 359

Query: 361 TKPGLPVVNADGTPKWRMAPGPNGPYWKQGMQNGYQDVGSWTFFKDHDANKTAAAWLYAQ 420
           TK GLPVVNADG+PKWRMAP P GPYWKQGMQNGYQDVGSWTFFK+ D N+ AAAWLYAQ
Sbjct: 360 TKKGLPVVNADGSPKWRMAPSPYGPYWKQGMQNGYQDVGSWTFFKNTDPNRLAAAWLYAQ 419

Query: 421 FVTAKTTSLKKTMVGLTPIRESDIQSKAMTDMAPKLGGLVEFYRSPARVAWSPTGTNVPD 480
           FVT+KT SLKK++ GLT IR+SDI  + +T  A + GGL+EFYRSPARVAW+PTGTNVPD
Sbjct: 420 FVTSKTVSLKKSLTGLTFIRDSDIHHEYLTKNAAQYGGLIEFYRSPARVAWTPTGTNVPD 479

Query: 481 YPKLAQLWWKNVAQAVTGEKTPQGAMDTLADEMDQVMARLERAGMAHCAPKLNAKSDPNK 540
           YPKLAQLWWKNVA AVTGEKTPQ AMD LA+EMDQVM RL+RAGM +CAPKLN K DP K
Sbjct: 480 YPKLAQLWWKNVATAVTGEKTPQAAMDNLAEEMDQVMGRLQRAGMTNCAPKLNPKGDPAK 539

Query: 541 WLSDKQAPWKKLANEKPKGETIAYGTLLQAWKDGKTR 577
           WLSD  APWKKLANEKPKGETIAY  LLQAWK+GK R
Sbjct: 540 WLSDDHAPWKKLANEKPKGETIAYDKLLQAWKEGKVR 576


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: 1454
Number of extensions: 77
Number of successful extensions: 1
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: 576
Length adjustment: 36
Effective length of query: 541
Effective length of database: 540
Effective search space:   292140
Effective search space used:   292140
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