GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08235 in Jannaschia aquimarina GSW-M26

Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate WP_043917488.1 jaqu_RS03105 urea ABC transporter permease subunit UrtB

Query= reanno::azobra:AZOBR_RS08235
         (301 letters)



>NCBI__GCF_000877395.1:WP_043917488.1
          Length = 652

 Score =  134 bits (336), Expect = 7e-36
 Identities = 91/294 (30%), Positives = 155/294 (52%), Gaps = 22/294 (7%)

Query: 9   INGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGITWVPLA 68
           ++ LSL +IY L AIG  + +G++G+IN AHGE  MIGA+   +  L +         L+
Sbjct: 363 LDALSLASIYFLAAIGLAVTFGVMGVINMAHGEFIMIGAYTGYVVQLFVPD-----YTLS 417

Query: 69  LLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQILQGARSKP 128
           L++ L  +     + G  +ER+  R L   P L  L++  G+S+ LQ   + + G +++P
Sbjct: 418 LVIALPLAFCTAGLAGVALERLVIRHLMHRP-LETLLATFGISVALQQIAKNVFGTQARP 476

Query: 129 L-QPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRACEQDKKMA 187
           L  P        +   +SVS++R+A  V+ +  +     ++ RT LG   RA  Q+  MA
Sbjct: 477 LTSPDWLAGSWQISEVISVSWIRVAIFVLALIFLAAIVYVLRRTRLGLEVRAVTQNPGMA 536

Query: 188 GLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAVLGGIGSL 247
             +G++  R+  LTF +G+ +A VAG+ + L Y  +   +G    V++F   V+GG+GS+
Sbjct: 537 ASMGIDPGRIGMLTFGLGSGIAGVAGVAIGL-YAQVTSEMGAGYIVQSFMTVVVGGVGSV 595

Query: 248 PGAMLGGVVIGLIEAFWSGYMGSEW----KDVATFTILVLVLI----FRPTGLL 293
            G + G  +IG ++       G EW      +A  T ++L +I    FRP G++
Sbjct: 596 FGTLAGAGLIGGLQ------KGIEWLNPSNTLAAQTFMILFIIAFIQFRPRGIV 643


Lambda     K      H
   0.329    0.144    0.425 

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: 423
Number of extensions: 26
Number of successful extensions: 4
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: 301
Length of database: 652
Length adjustment: 32
Effective length of query: 269
Effective length of database: 620
Effective search space:   166780
Effective search space used:   166780
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: 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