GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ppa in Magnetospirillum magneticum AMB-1

Align Phenylacetate permease, Ppa (characterized)
to candidate WP_011385106.1 AMB_RS13720 cation acetate symporter

Query= TCDB::O50471
         (520 letters)



>NCBI__GCF_000009985.1:WP_011385106.1
          Length = 561

 Score =  678 bits (1750), Expect = 0.0
 Identities = 340/522 (65%), Positives = 419/522 (80%), Gaps = 3/522 (0%)

Query: 2   NWTAISMFMVFVCFTLLVTRWAALRTRSASDFYTAGGGLTGMQNGLAIAGDMISAASFLG 61
           NW AI MF++FV  TL +T WAA RT++A+DFY AGGG+TG QNGLAIAGD +SAASFLG
Sbjct: 40  NWHAIIMFVIFVGMTLGITYWAAGRTKTAADFYAAGGGITGFQNGLAIAGDYMSAASFLG 99

Query: 62  ISAMMFMNGYDGLLYALGVLAGWPIILFLIAERLRNLGKYTFADVVSYRLAQTPVRLTSA 121
           ISA+++ +GYDGL++++G L GWPIILFLIAERLRNLGKYTFADV  YRLA+TP+R  +A
Sbjct: 100 ISALVYGSGYDGLIFSVGWLVGWPIILFLIAERLRNLGKYTFADVCGYRLARTPIRTFAA 159

Query: 122 FGTLVVALMYLVAQMVGAGKLIELLFGISYLYAVMLVGVLMVAYVTFGGMLATTWVQIIK 181
            G+L+V + YL+ QMVGAG+LI+LLFG+ Y+YAVM+VG LM+ YVTFGGM+ATTWVQIIK
Sbjct: 160 TGSLIVVIFYLIGQMVGAGQLIKLLFGMDYIYAVMIVGALMMVYVTFGGMVATTWVQIIK 219

Query: 182 AVMLLSGTSFMAFMVLKHFGFSTEAMFASAVAVHAKGQAIMAPGGLLSNPVDAISLGLGM 241
           A +LL G +F+AF V+ HFGFS E +F  A+ VH K  AIMAPG L++NPVDAISLG+ +
Sbjct: 220 ACLLLGGATFIAFGVMSHFGFSFEKLFVKAIEVHPKKVAIMAPGALVTNPVDAISLGMAL 279

Query: 242 MFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYLLLIVIGFGAIVMVGTEPSY-R 300
           MFGTAGLPHILMRFFTV DA+EARKSVFYATGFIGYFY+L  +IGFGAI +V T P Y  
Sbjct: 280 MFGTAGLPHILMRFFTVPDAREARKSVFYATGFIGYFYILTFIIGFGAITLVATNPEYLT 339

Query: 301 DATGA--IIGGGNMIAVHLAQAVGGNLFLGFISAVAFATILAVVAGLALSGASAVSHDLY 358
              G+  + GG NM AV LA A+GG+LFLGFISAVAFATILAVV+GL L+GASA+SHDLY
Sbjct: 340 KGLGSLDLKGGNNMAAVWLAHAIGGDLFLGFISAVAFATILAVVSGLTLAGASAISHDLY 399

Query: 359 ACVIRQGKATEQEEMRVSRIATLLIGLLAVLLGLMFESQNIAFLSGLVLAVAASVNFPVL 418
           A VI  G+ATE  E+ VS+IA++ +G++AVLLGL+FE QN+AF+  L  +VAAS NFPVL
Sbjct: 400 ASVIMHGQATEGREVTVSKIASIGLGIIAVLLGLVFEKQNVAFIVALTFSVAASANFPVL 459

Query: 419 LLSMFWKGLTTRGAVCGSMAGLASAVLLVVLGPAVWVNVLHHEKALFPYSNPALFSMSLA 478
           +LSMFW GLTTRGAV G M GL  +V++VVL  AVWV     +  +FP++ PALFS+  A
Sbjct: 460 VLSMFWGGLTTRGAVLGGMIGLLMSVIMVVLSKAVWVQSFGFKAEIFPFAYPALFSVPAA 519

Query: 479 FLSAWVFSVTDSSERASEERGRYLAQFIRSMTGIGAAGASKH 520
           F  +W+FS+ D+S +A  ER  Y AQ IRS TG+GA GA+ H
Sbjct: 520 FFFSWLFSILDNSPQAQAERAAYEAQSIRSETGLGAEGAASH 561


Lambda     K      H
   0.328    0.139    0.407 

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: 951
Number of extensions: 41
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: 520
Length of database: 561
Length adjustment: 35
Effective length of query: 485
Effective length of database: 526
Effective search space:   255110
Effective search space used:   255110
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 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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