GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Burk376:H281DRAFT_02180 H281DRAFT_02180 amino
           acid/polyamine/organocation transporter, APC superfamily
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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