GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ga0059261_1577 in Paraburkholderia bryophila 376MFSha3.1

Align L-glutamine and L-histidine transporter (characterized)
to candidate H281DRAFT_02180 H281DRAFT_02180 amino acid/polyamine/organocation transporter, APC superfamily

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



>FitnessBrowser__Burk376:H281DRAFT_02180
          Length = 463

 Score =  364 bits (934), Expect = e-105
 Identities = 196/466 (42%), Positives = 280/466 (60%), Gaps = 17/466 (3%)

Query: 5   LFRTKRVKDA-AEQAPEHRLAATLSWPHLVALGVGAIVGTGILTLIGVGAGKAGPAVIMS 63
           LFR K V+   A  A    L   L    L  LGVGAI+GTGI  L G GA +AGPA+++S
Sbjct: 3   LFRKKSVEHMIATSAQNAGLKKALGALDLTFLGVGAIIGTGIFVLTGTGAVQAGPALMVS 62

Query: 64  FVIAGAICACAALAYAEMATMMPASGSAYAYSYAVLGEIIAWVVGWSLILEYSLVVSTVA 123
           F+IA   C  AALAYAE A+ +P +GS Y YSYA LGE+ AW++GW L+LEY L  S V+
Sbjct: 63  FLIAAVACGFAALAYAEFASTIPVAGSIYTYSYATLGELAAWIIGWDLMLEYGLATSAVS 122

Query: 124 VGWSGYAAPLLHAW-TGMPLELMAGPHA----NGIVNLPAIFIIAVVAGLLCLGTKESAT 178
           VGWSGY   LL  +   +P+ L A P A      + NLPA  ++  +  LL +G +ESA 
Sbjct: 123 VGWSGYLQSLLSGFGVSLPVALTAAPGALPGHETLFNLPAFLVMMAITALLSVGVRESAR 182

Query: 179 LNAALVVVKIIALAVFVAVALPYFNGANLEPFAPFGFAKTISPDGVERGVMAAAAIIFFA 238
           +N  +V +K++ + + +AV + +   AN  PF P G+           GV  AAA++FFA
Sbjct: 183 INNIMVAIKVVVVLLVIAVGVFHVTPANWHPFMPNGW----------NGVFGAAAVMFFA 232

Query: 239 FYGFDAISTAAEETKNPGRDLAIGIVGSMIACVAIYMLVAVAAVGATPFTHFANSPEPLA 298
           F GFD++S+AAEE KNP RDL IGI+ S+  C  +Y+ VA    G  P   FAN   P++
Sbjct: 233 FIGFDSVSSAAEEVKNPKRDLPIGIIASLGVCAVLYVAVAAVVTGIVPSAQFANISHPVS 292

Query: 299 LILRDLGRPGFATFLAVSAIIALPTVLLGFLFGQSRIFFTMARDGMLPIGLAKVSKR-GS 357
             L+  G+   A F+ + A++ + TV+L   +GQ+R+ F M+RDG+LP  L++V  R  +
Sbjct: 293 YALQVAGQKWVAGFIDLGAVLGMLTVILVMAYGQTRVIFAMSRDGLLPARLSRVHPRFAT 352

Query: 358 PVRITLFTAAIVAVIAGLLPIDEIAALANAGTLAAFTAVAVCMMVLRVRAPDMPRMFRTP 417
           P   T        +I  L+P++ +A L N GTLAAF+ V++ ++VLR   P++PR FR P
Sbjct: 353 PFFTTWLVGIFFGLIGALVPLNVLAELINIGTLAAFSMVSIAVLVLRKTHPELPRAFRCP 412

Query: 418 LWWLVGAIAVLGCIYLFFSLPVKTQLWFLAWNALGVVIYFAYARPR 463
              +V  +AV  C++L  +L   T + F+ W  +G+VIYF Y+R R
Sbjct: 413 GVPVVPVLAVASCVFLMANLQAVTWVAFVVWLLIGMVIYFGYSRRR 458


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: 637
Number of extensions: 37
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: 470
Length of database: 463
Length adjustment: 33
Effective length of query: 437
Effective length of database: 430
Effective search space:   187910
Effective search space used:   187910
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 17 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