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_102938052.1 B1812_RS04230 amino acid permease

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



>NCBI__GCF_002117405.1:WP_102938052.1
          Length = 481

 Score =  313 bits (803), Expect = 6e-90
 Identities = 175/465 (37%), Positives = 260/465 (55%), Gaps = 30/465 (6%)

Query: 14  AAEQAPEHRLAATLSWPHLVALGVGAIVGTGILTLIGVGAGK-AGPAVIMSFVIAGAICA 72
           A   A E+ L   L W  L+A+G+G I+G GI  L G  A   AGP V +SF+++G  C 
Sbjct: 20  AENDAEENGLKRALGWASLMAMGIGGIIGAGIFVLTGQAAADYAGPGVTISFLLSGLACT 79

Query: 73  CAALAYAEMATMMPASGSAYAYSYAVLGEIIAWVVGWSLILEYSLVVSTVAVGWSGYAAP 132
             AL YAE+A ++PA+GS Y Y+Y  LGEI AW++GW+L+LEY+   +TVAVGW+GY   
Sbjct: 80  FVALCYAELAALIPAAGSTYTYTYVTLGEIFAWIIGWNLVLEYAAGAATVAVGWAGYFNR 139

Query: 133 L-----LHAWTGMPLELMAGPHA----NGIVNLPAIFIIAVVAGLLCLGTKESATLNAAL 183
           +     +H    +     A  H+    +G+ N+PA  II ++  LL  GT ES+  N  +
Sbjct: 140 VMQGLGIHLPEALTSAYFANAHSIGGTHGVFNVPAAAIILLLTALLMRGTSESSFFNNII 199

Query: 184 VVVKIIALAVFVAVALPYFNGANLEPFAP--------FGFAKTISPDGVERGVMAAAAII 235
           VV+K++ + V + V   + + AN  P  P        FG++          GV+  A+++
Sbjct: 200 VVIKVMVVLVVIFVGAAHVDAANWTPLIPENTDHFGHFGWS----------GVVRGASVV 249

Query: 236 FFAFYGFDAISTAAEETKNPGRDLAIGIVGSMIACVAIYMLVAVAAVGATPFTHFANSPE 295
           FFA+ GFD +STAA+E   P RD+ IGI+GS++ C  +Y+ VA  A G   +      P+
Sbjct: 250 FFAYIGFDGVSTAAQEAHTPQRDVPIGILGSLVICTILYVAVAAVATGVVSYKEL-GVPD 308

Query: 296 PLALILRDLGRPGFATFLAVSAIIALPTVLLGFLFGQSRIFFTMARDGMLPIGLAKVSK- 354
           P+AL++   G    +  + + AI  L T +L  LFGQ+RIF+ MA+DG+LP   A V   
Sbjct: 309 PMALVMDRTGVAWLSWVVKLGAIAGLTTAILLLLFGQTRIFYAMAQDGLLPKVFAAVHPV 368

Query: 355 RGSPVRITLFTAAIVAVIAGLLPIDEIAALANAGTLAAFTAVAVCMMVLRVRAPDMPRMF 414
             +P          VA+ AGL PI+ +  + + GTLAAF  V   ++ LR   PDM R F
Sbjct: 369 WRTPAVSQALVGVFVALAAGLFPINILDEMVSIGTLAAFALVCGAVLHLRRSQPDMHRPF 428

Query: 415 RTPLWWLVGAIAVLGCIYLFFSLPVKTQLWFLAWNALGVVIYFAY 459
           R P    +  + +  C+ L  +LP++T L  + W A+G+ IYF Y
Sbjct: 429 RAPGIPAMPLLGIASCLALMVALPLETWLRLIVWTAIGMAIYFFY 473


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: 635
Number of extensions: 27
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: 481
Length adjustment: 33
Effective length of query: 437
Effective length of database: 448
Effective search space:   195776
Effective search space used:   195776
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