GapMind for catabolism of small carbon sources

 

Aligments for a candidate for N515DRAFT_2924 in Dyella japonica UNC79MFTsu3.2

Align Basic amino acid/polyamine antiporter, APA family (characterized, see rationale)
to candidate N515DRAFT_2925 N515DRAFT_2925 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)

Query= uniprot:A0A1I1Y8J0
         (492 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_2925 N515DRAFT_2925 amino
           acid/polyamine/organocation transporter, APC superfamily
           (TC 2.A.3)
          Length = 480

 Score =  540 bits (1391), Expect = e-158
 Identities = 261/490 (53%), Positives = 345/490 (70%), Gaps = 13/490 (2%)

Query: 1   MLKNLFAT-TQISPASADLPGGGAHGEATLKRALTARHLVLLGIGAIIGAGIFVITGQAA 59
           MLK LFA  T  S A         HG  +L+R L    +  LGIGA+IG GIFV+TGQAA
Sbjct: 1   MLKQLFARKTDFSDAD------DCHGGPSLRRTLGKWGITALGIGAVIGTGIFVVTGQAA 54

Query: 60  AEHAGPAIVLSFVFAGIACALAALCYAEFAAMLPVSGSAYSYSYATLGEYVAWFVGWSLV 119
           AEHAGPA+++SF+ A I     ALCYAEFA ++P+SGS+YSY+YATLGE VAWF+GW++V
Sbjct: 55  AEHAGPAVLISFMLAAICSGFTALCYAEFATLIPISGSSYSYAYATLGELVAWFIGWNMV 114

Query: 120 LEYLFTVATVAAGWSGYFNKLLALISGWIGHDVSLPQTLAAAPFTVVDGHIQATGMFINL 179
           LEY  + + VAA W+GYF  LL  +       + LP  L  AP    DGH+  TG  +NL
Sbjct: 115 LEYGISASAVAASWTGYFTSLLDHVG------IHLPVALTEAPLAFKDGHLVTTGHLLNL 168

Query: 180 PAVAIIAAITGLCYVGITQSAFVNSIIVAIKVTVILLFIAFATKYINPDNWHPFIPASEG 239
           PAVAI+ A+T LCYVGI +S+ +N ++VA+KV +I++ +    +Y++P NWHPFIPA + 
Sbjct: 169 PAVAIVLALTWLCYVGIRESSGLNVLMVALKVGLIIVVVVAGYRYVDPANWHPFIPAEQE 228

Query: 240 ASKYGWAGVGRAAAIVFFSYIGFDAVSTAAGEAKNPQRDMPIGIIGSLILCTILYIIVAG 299
             KYGW+G+ R AA+VFF+YIGF+A STAA E KNPQ+D+P G + SL++CT+LY+ +A 
Sbjct: 229 PGKYGWSGIMRGAAMVFFAYIGFEATSTAAQECKNPQKDLPFGTLVSLVICTVLYLAMAA 288

Query: 300 ILTGIADFRLLGTPEPVSTALDNYPSLHWLQIIVVIGAVTGLSSVMLVMLMGQPRIFYSM 359
           +LTG+  +  LGT EPV TA+ N+P L WL+++V IGA+ GLSSV+LVM++ QPRIF  M
Sbjct: 289 VLTGLIPYTELGTSEPVVTAIRNHPELGWLRLVVEIGAMIGLSSVILVMIIAQPRIFMIM 348

Query: 360 ARDGLIPAVFGRIHQKFRTPHVGTVVVGVLAAALGGLFNIGVLGEMVAMGTLLAFATVCI 419
           +RDGL+P VF RIH K RTPH+ TV+ G+  A L  +F + +L ++ +MGTL+AF  VC 
Sbjct: 349 SRDGLLPPVFNRIHPKHRTPHLNTVITGIGIAILAAVFPLDLLADLTSMGTLIAFVAVCA 408

Query: 420 GVLVLRYTRPELPRAFRVPVPWIVCPLGALACMALFLQSFLEHWRWMLAWIAIGQAIYFL 479
           GVL+LRYT PELPR FRVP  W VC  G  +C+AL       +W  M+ W AIG AIYF 
Sbjct: 409 GVLILRYTAPELPRLFRVPAAWFVCTAGVFSCLALLYFMAWFNWLLMIIWTAIGLAIYFG 468

Query: 480 YGYSHSKLRK 489
           YG  HS+LR+
Sbjct: 469 YGMRHSRLRR 478


Lambda     K      H
   0.328    0.141    0.441 

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: 818
Number of extensions: 42
Number of successful extensions: 2
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: 492
Length of database: 480
Length adjustment: 34
Effective length of query: 458
Effective length of database: 446
Effective search space:   204268
Effective search space used:   204268
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: 52 (24.6 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, 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