GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ga0059261_1577 in Dyadobacter tibetensis Y620-1

Align L-glutamine and L-histidine transporter (characterized)
to candidate WP_025765060.1 X939_RS0120010 amino acid permease

Query= reanno::Korea:Ga0059261_1577
         (470 letters)



>NCBI__GCF_000566685.1:WP_025765060.1
          Length = 484

 Score =  347 bits (889), Expect = e-100
 Identities = 186/485 (38%), Positives = 290/485 (59%), Gaps = 34/485 (7%)

Query: 1   MAGGLFRTKRVKDAAEQAP--EHRLAATLSWPHLVALGVGAIVGTGILTLIGVGAGK-AG 57
           MA  L+  K ++   +++   E++L  +LS   LVALG+GAI+G G+ +L G+ A + +G
Sbjct: 1   MASQLWFKKPIEKLLQESTGEENQLKRSLSSLSLVALGIGAIIGAGLFSLTGIAAAEHSG 60

Query: 58  PAVIMSFVIAGAICACAALAYAEMATMMPASGSAYAYSYAVLGEIIAWVVGWSLILEYSL 117
           PAV +SF++A   C  A L YAE A+M+P +GSAY YSYA +GE +AW++GW L+LEY+L
Sbjct: 61  PAVTISFIVAAVGCGFAGLCYAEFASMIPIAGSAYTYSYATMGEFVAWIIGWDLVLEYAL 120

Query: 118 VVSTVAVGWSGYAAPLLHAWT-GMPLELMAGPHA-----------NGIVNLPAIFIIAVV 165
             +TV+V WS Y    L  +   +P +L++ P             NGI+NLPAI I+ ++
Sbjct: 121 GAATVSVSWSRYLLEFLSKFDIHLPTQLVSSPFEVLTLSDGTIIDNGIINLPAILIVWML 180

Query: 166 AGLLCLGTKESATLNAALVVVKIIALAVFVAVALPYFNGANLEPFAP--------FGFAK 217
           + LL  GT+ SA LN  LV++K+  + +F+ +   + N  N  P+ P        FG++ 
Sbjct: 181 SLLLIRGTEGSAYLNNFLVILKVAVVLIFIGLGWSHINPENYVPYIPENTGNYENFGWS- 239

Query: 218 TISPDGVERGVMAAAAIIFFAFYGFDAISTAAEETKNPGRDLAIGIVGSMIACVAIYMLV 277
                    G+   AA++FFAF GFDA+STAA+E KNP + + IGI+GS+I C  +Y+L 
Sbjct: 240 ---------GIATGAAVVFFAFIGFDAVSTAAQEAKNPQKGMPIGILGSLIVCTILYVLF 290

Query: 278 AVAAVGATPFTHFANSPEPLALILRDLGRPGFATFLAVSAIIALPTVLLGFLFGQSRIFF 337
           A    G   +  FAN  +P A      G     T L V+ +    +V+L  L GQSR+F+
Sbjct: 291 AHVMTGLVNYKEFANDAKPAATAFAATGYDSLQTGLIVAILAGYTSVMLVMLLGQSRVFY 350

Query: 338 TMARDGMLPIGLAKV-SKRGSPVRITLFTAAIVAVIAGLLPIDEIAALANAGTLAAFTAV 396
           +M++DG+LP   +++  K  +P +  +F    V++ AG +P+ ++  + + GTL AF+ V
Sbjct: 351 SMSKDGLLPKFFSEIHPKFSTPWKTNIFFMLFVSIFAGFVPVSDLGHMVSIGTLFAFSLV 410

Query: 397 AVCMMVLRVRAPDMPRMFRTPLWWLVGAIAVLGCIYLFFSLPVKTQLWFLAWNALGVVIY 456
            V + +LRV+ PD+PR FRTPL   V  + ++ C+YL +SLP+++      W ALG+ IY
Sbjct: 411 CVGVWMLRVKRPDLPRSFRTPLVPFVPLMGIIVCVYLMYSLPIESWYRLAIWLALGLAIY 470

Query: 457 FAYAR 461
           F Y +
Sbjct: 471 FFYGK 475


Lambda     K      H
   0.327    0.140    0.426 

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: 662
Number of extensions: 35
Number of successful extensions: 6
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: 470
Length of database: 484
Length adjustment: 33
Effective length of query: 437
Effective length of database: 451
Effective search space:   197087
Effective search space used:   197087
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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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