GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21720 in Rhizorhabdus wittichii RW1

Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate WP_012048835.1 SWIT_RS13330 ABC transporter permease subunit

Query= reanno::pseudo5_N2C3_1:AO356_00470
         (220 letters)



>NCBI__GCF_000016765.1:WP_012048835.1
          Length = 374

 Score = 82.4 bits (202), Expect = 1e-20
 Identities = 70/202 (34%), Positives = 91/202 (45%), Gaps = 23/202 (11%)

Query: 17  TLWAGFLTSVQ-CSLLAIVLGTLIGLVAGLVLTYGRTWMRAPFRFYVDLIRGTPVFVLVL 75
           T W G L     C+L  IV G+ + +V  L L          F F   L   TP FV VL
Sbjct: 190 TAWRGHLHKASLCTLGTIVAGSALWIVLDLGLARDVPHFDR-FNFTGGLTL-TPEFVAVL 247

Query: 76  ACFYMAPALGWQIGAFQAGVLGLTLFCGSHVAEIVRGALQALPRGQMEASQAIGLTFYQS 135
                     W          G  ++  +  AEIVRG L  +PRGQ EAS+A+GL+  QS
Sbjct: 248 ----------W----------GSVIYASAFAAEIVRGGLDGVPRGQWEASRALGLSKRQS 287

Query: 136 LGYVLLPQALRQILPTWVNSSTEIVKASTLLSVIGVAELLLSTQQIIARTFMTLEFYLFA 195
           L  V++PQALR I+P   +    I+K STL  V+G  +L       I  T   LE     
Sbjct: 288 LRLVIVPQALRMIVPPMNSQFITILKNSTLALVVGYPDLNFVANTAINHTGQGLEGVAIL 347

Query: 196 GFLFFIINYAIELLGRHIEKRV 217
             +FF +  AI L    +  RV
Sbjct: 348 MLVFFTLASAISLAMNRLNARV 369



 Score = 32.7 bits (73), Expect = 9e-06
 Identities = 23/64 (35%), Positives = 32/64 (50%), Gaps = 4/64 (6%)

Query: 16  DTL-WA---GFLTSVQCSLLAIVLGTLIGLVAGLVLTYGRTWMRAPFRFYVDLIRGTPVF 71
           DT+ WA   G   S+  +LL IVL T+ G+   L    G    R     +VDL+R  P+ 
Sbjct: 69  DTIAWAFVVGLGNSIALTLLIIVLSTMAGVPIALARHSGHMLARTLAGGFVDLVRNVPLV 128

Query: 72  VLVL 75
           V +L
Sbjct: 129 VQLL 132


Lambda     K      H
   0.330    0.142    0.443 

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: 222
Number of extensions: 11
Number of successful extensions: 2
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: 220
Length of database: 374
Length adjustment: 26
Effective length of query: 194
Effective length of database: 348
Effective search space:    67512
Effective search space used:    67512
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 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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