GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcP in Mariniradius saccharolyticus AK6

Align D-fructose transporter, sugar porter family (characterized)
to candidate WP_008629477.1 C943_RS15175 sugar porter family MFS transporter

Query= reanno::Korea:Ga0059261_1777
         (458 letters)



>NCBI__GCF_000330725.2:WP_008629477.1
          Length = 447

 Score =  374 bits (961), Expect = e-108
 Identities = 208/438 (47%), Positives = 291/438 (66%), Gaps = 13/438 (2%)

Query: 21  AIILSAAGAALGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTVASALIGTVLGSLIAG 80
           A+ LS   AALGG LFGFDTAVISGA + +Q  + L D   G  VA AL GTVLG+L+ G
Sbjct: 7   ALFLSIT-AALGGFLFGFDTAVISGAERDIQNLWELDDWSHGLAVAMALYGTVLGALLGG 65

Query: 81  APADRFGRKGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGAASVVTPIYIAEV 140
            PAD++GRK  ++ + I Y VS+LG+ L  D+ +F+ +RF+GGL +GA+SVV P+YI+E+
Sbjct: 66  IPADKYGRKVTLIWIGIFYFVSALGSALVDDVYSFMFYRFIGGLGVGASSVVAPMYISEI 125

Query: 141 SPARFRGRLVAMNQLNIVLGILIAFLSNYIIAGLVQYDVAWRWMFGIVAVPSTIFLLVTL 200
           +PA+ RG+LVA+ Q NIV GIL+A+ SNY+I G    D AWRWM G+ A+P+ I+ ++ L
Sbjct: 126 APAKSRGQLVALYQFNIVFGILMAYFSNYLI-GTANLDEAWRWMLGVEAIPALIYSILIL 184

Query: 201 LLPESPRWLAIHGQ-ADRARDVMQRLGFADPRAELARIELA-EAREEAAGK---PRLFQR 255
            +P+SPRWL    Q    AR+++ R    DP      I+LA E  +   GK     LF  
Sbjct: 185 KVPKSPRWLIAKKQDYQTAREILTR---TDPEGVDEAIKLAIEESKSIKGKTSVAALFD- 240

Query: 256 SHFTPVA-CAIAIAMFNQLSGINALLYYAPRIFELAGAGADSALLQSIAVGGTNLVFTVA 314
           S F  ++  A  +A FNQ+SGINA++Y+APRIFE AG   + AL  +I +G  NL+ T+A
Sbjct: 241 SRFRKISFFAFLMAFFNQMSGINAIIYFAPRIFESAGISTEDALFSTIGIGVINLIATMA 300

Query: 315 ALFLIDRFGRRPLLFVGSVICAATLLLVGWQLESAKPDGTLILFGLLGFIAAFAMSQGAV 374
            L+LID+ GR+ L+++GSV    +L L+ +          L+ + +  FIA+ A+ QG+V
Sbjct: 301 GLYLIDKLGRKKLMYIGSVGYIISLSLMAYSYFGGMISSNLLPYFVFVFIASHAIGQGSV 360

Query: 375 IWVFISEVFPSAVRGKGQALGSTTHWVMAAAITWAFPVFAASVG-GWVFAFFGAMMLLQL 433
           IWVFI+E+FP+ +R  GQ+LGS THW++AA I   FP FA + G G +FAFF  MM+LQL
Sbjct: 361 IWVFIAEIFPNELRAFGQSLGSFTHWILAALIANVFPFFANTFGAGSIFAFFALMMVLQL 420

Query: 434 LWTWKFMPETNGIALEDM 451
           LW    MPET G +LE++
Sbjct: 421 LWVAFRMPETKGKSLEEI 438


Lambda     K      H
   0.327    0.139    0.420 

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: 618
Number of extensions: 41
Number of successful extensions: 7
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: 458
Length of database: 447
Length adjustment: 33
Effective length of query: 425
Effective length of database: 414
Effective search space:   175950
Effective search space used:   175950
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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