GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ga0059261_1577 in Methylocystis bryophila S285

Align L-glutamine and L-histidine transporter (characterized)
to candidate WP_085770386.1 B1812_RS03615 amino acid permease

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



>NCBI__GCF_002117405.1:WP_085770386.1
          Length = 488

 Score =  315 bits (807), Expect = 2e-90
 Identities = 180/463 (38%), Positives = 266/463 (57%), Gaps = 17/463 (3%)

Query: 5   LFRTKRVKDAAEQAPEH-RLAATLSWPHLVALGVGAIVGTGILTLIGV-GAGKAGPAVIM 62
           LFR K ++    +A E   L   L    LV +G+G ++G GI  L GV  A +AGP V +
Sbjct: 6   LFRAKSIESLQAEALERGALRRALGLWQLVGIGLGGLIGVGIFVLTGVVAATQAGPGVAL 65

Query: 63  SFVIAGAICACAALAYAEMATMMPASGSAYAYSYAVLGEIIAWVVGWSLILEYSLVVSTV 122
           SF+IAG     AAL YAE A+M+P +GSAY Y+YAVLGE+ AW++GW L+LEY+LVV+ V
Sbjct: 66  SFLIAGVASGAAALCYAEFASMLPVAGSAYTYAYAVLGELPAWIIGWDLLLEYALVVAVV 125

Query: 123 AVGWSGYAAPLLHAWTGMPLELMAGPHANG---IVNLPAIFIIAVVAGLLCLGTKESATL 179
           ++GWSGY   LL  +   P E  AG    G   I++L A+     VA LL L  +  A  
Sbjct: 126 SIGWSGYLRALLALFGVAPPEWAAGAPGTGDGHILDLFAMLGAFGVALLLTLRVEWGARF 185

Query: 180 NAALVVVKIIALAVFVAVALPYFNGANLEPFAPFGFAKTISPDGVERGVMAAAAIIFFAF 239
           N A+V++KI A+ V +  A P+ N AN  PF PFGF           GV+  AA++FFA 
Sbjct: 186 NTAMVLLKIAAVIVVILAAAPHINPANWRPFMPFGFG----------GVVEGAAVVFFAV 235

Query: 240 YGFDAISTAAEETKNPGRDLAIGIVGSMIACVAIYMLVAVAAVGATPFTHFANSPEPLAL 299
           +G+D ++TA EE   P RDL   ++ S++  + +Y+L+++A  G   +    N+  P+A 
Sbjct: 236 FGYDTLTTAGEEALEPQRDLPRAVLLSLVVSLTLYILMSLALTGIARYDTLDNA-APVAS 294

Query: 300 ILRDLGRPGFATFLAVSAIIALPTVLLGFLFGQSRIFFTMARDGMLPIGLAKVSKR-GSP 358
               LG       ++ +A++ + +V+L FL G +RI+F M+RDG+LP   A+   +  +P
Sbjct: 295 AFAALGMGWATLVVSAAAVVGILSVMLAFLLGCARIWFAMSRDGLLPAWFARPHPQFATP 354

Query: 359 VRITLFTAAIVAVIAGLLPIDEIAALANAGTLAAFTAVAVCMMVLRVRAPDMPRMFRTPL 418
            R TL    + A+++   PI E+A L N GTL+AF  + + ++ LR   PD+PR FR PL
Sbjct: 355 YRPTLIAGGLCALVSAFFPIREVAELVNIGTLSAFVVICLAVIALRHTRPDVPRGFRAPL 414

Query: 419 WWLVGAIAVLGCIYLFFSLPVKTQLWFLAWNALGVVIYFAYAR 461
              +  I V   ++L   LP      F+ W  +G+ +YF Y R
Sbjct: 415 SPYLPLIGVGFSLWLLSKLPAIAWERFVVWLIIGLAVYFLYGR 457


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: 730
Number of extensions: 55
Number of successful extensions: 9
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: 488
Length adjustment: 34
Effective length of query: 436
Effective length of database: 454
Effective search space:   197944
Effective search space used:   197944
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 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