GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapQ in Brucella inopinata BO1

Align AapQ, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate WP_008511689.1 BIBO1_RS19985 amino acid ABC transporter permease

Query= TCDB::Q52813
         (400 letters)



>NCBI__GCF_000182725.1:WP_008511689.1
          Length = 323

 Score = 90.9 bits (224), Expect = 5e-23
 Identities = 89/290 (30%), Positives = 136/290 (46%), Gaps = 43/290 (14%)

Query: 98  NTLLVAVTGIFTATIIGFLIG--IGRLSRNWLIAKLCTVYVEVFRNIPPLLVIFFWYLGV 155
           N ++      F+ ++I FL    + RLSRN    ++  V+ E+F     LL+IFF+    
Sbjct: 53  NPVVARALSAFSISLILFLNWKLLKRLSRN---QQVVAVWTELF----VLLMIFFY---- 101

Query: 156 LSVLPQPRESVGLPFSMYLNNRGLAFPKPIFDT---GMIAVGIALVIAIVASIIIARWAH 212
                    S  L FS           +    T     I++ IA +IA++ +I     A 
Sbjct: 102 ---------SFDLSFSFIARKISFLITQGTVTTLYISAISIAIATIIALIGAI-----AK 147

Query: 213 KRQAATGQPFHTVWTAIALIVGLPLLVFVVSGFPLTFDVPVAGKFNLTGGSVVGPEFMSL 272
             Q        T +T+  L  GLPLL+ +   + +   +P  G   + G    G      
Sbjct: 148 LSQNGVIYGLSTFYTS--LFRGLPLLMQI---YIIYLGLPQIGY--VIGAIPAG------ 194

Query: 273 FLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVVPQALRIIIPPLTS 332
            LALS    +++ EI R GI  +P GQ EAA ALGL  +    LV++PQA+RIIIPP  +
Sbjct: 195 ILALSLCYGAYMTEIFRAGIESIPHGQKEAATALGLGSAQTMWLVILPQAMRIIIPPTGN 254

Query: 333 QYLNLTKNSSLAIAIGFSDLVAVGGTILNQSGQAIEIVCIWGIVYLSLSI 382
           Q++ + K+SSL   IG  +L+ V  T      + IE++    ++Y  LSI
Sbjct: 255 QFIAMLKDSSLVSVIGVWELMYVARTQGQTEFRHIEMLITASMIYWILSI 304



 Score = 48.1 bits (113), Expect = 4e-10
 Identities = 28/86 (32%), Positives = 45/86 (52%), Gaps = 6/86 (6%)

Query: 95  GILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFRNIPPLLVIFFWYLG 154
           G + TL ++   I  ATII  +  I +LS+N +I  L T Y  +FR +P L+ I+  YLG
Sbjct: 121 GTVTTLYISAISIAIATIIALIGAIAKLSQNGVIYGLSTFYTSLFRGLPLLMQIYIIYLG 180

Query: 155 ------VLSVLPQPRESVGLPFSMYL 174
                 V+  +P    ++ L +  Y+
Sbjct: 181 LPQIGYVIGAIPAGILALSLCYGAYM 206


Lambda     K      H
   0.327    0.141    0.432 

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: 359
Number of extensions: 23
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: 400
Length of database: 323
Length adjustment: 29
Effective length of query: 371
Effective length of database: 294
Effective search space:   109074
Effective search space used:   109074
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: 49 (23.5 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