GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglG' in Rhodobacter viridis JA737

Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate WP_110804034.1 C8J30_RS01980 carbohydrate ABC transporter permease

Query= uniprot:A8LLL4
         (385 letters)



>NCBI__GCF_003217355.1:WP_110804034.1
          Length = 382

 Score =  468 bits (1204), Expect = e-136
 Identities = 240/384 (62%), Positives = 291/384 (75%), Gaps = 10/384 (2%)

Query: 2   DNIAGSKSSLTWAVQLSVVGLVVLWLLPTFGLFVSSFRTVEQISSSGWWKAMFPSEQNLT 61
           D  AG  ++L WAV ++   LV+LW +PT GL VSSFR  +QI +SGWW+A F S  N  
Sbjct: 7   DGAAGRSAALVWAVNIAAAALVLLWTIPTVGLLVSSFRDRDQIITSGWWRAAFSSTANDF 66

Query: 62  LRAADPDDFRMPQGDLFVVKGNLFEDEGISEAEISVWGTSSRDVAAYTAGETADLGDGET 121
           +RA    D ++ +GD+FV+ GN+      S+AE+  WG SS+  AAY  G+ A+L DG+ 
Sbjct: 67  VRAGTAAD-QVQEGDVFVISGNVLP----SKAELKSWGVSSKAPAAYQPGDIAELKDGQR 121

Query: 122 ITVQSNGAYVWSGTDDQISGRGQRVFVTATTPPEFTFANYENMLLDPNNSEGMARAFFNT 181
           +TV   G Y  +       GRG R+FVT   PP  T  NY  ++     +EG+ RAF NT
Sbjct: 122 LTVSDKGDYRLTSPTAFPEGRGMRIFVTTVAPPRLTTGNYARVI----TAEGIGRAFLNT 177

Query: 182 LTVTIPATIIPILVAAFAAYALAWMEFPGRALLIALIVGLLVVPLQLALIPLLTLHNAIG 241
           +TVTIPAT+IPIL+AAFAAYALAWM FPGRALL+A IVGLLVVPLQLALIPLL LHN IG
Sbjct: 178 MTVTIPATVIPILIAAFAAYALAWMRFPGRALLVATIVGLLVVPLQLALIPLLKLHNQIG 237

Query: 242 IGKGYLGTWLAHTGFGMPLAIYLLRNYMVGLPRDIIENAKVDGATDFQIFTKIVLPLSFP 301
           + + YLG WLAHTGFG+PLAIYLLRNYMVGLPR+IIE+A+VDGAT+FQIF +IVLPLSFP
Sbjct: 238 LNQSYLGIWLAHTGFGLPLAIYLLRNYMVGLPREIIESARVDGATEFQIFRRIVLPLSFP 297

Query: 302 ALASFAIFQFLWTWNDLLVAKVFLIDATGQTTVMTNQIVELLGTRGGNWEILATAAFVSI 361
           ALASFAIFQFLW WNDLLVA VFL +AT  T VMT  +  LLG+RGG+WEILA +AFVSI
Sbjct: 298 ALASFAIFQFLWVWNDLLVATVFLGNAT-DTQVMTGALRALLGSRGGDWEILAASAFVSI 356

Query: 362 AVPLLVFFSMQRFLVRGLLAGSVK 385
           AVPL+VFF++Q++LVRGLLAGSVK
Sbjct: 357 AVPLIVFFALQKYLVRGLLAGSVK 380


Lambda     K      H
   0.323    0.138    0.419 

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: 462
Number of extensions: 16
Number of successful extensions: 5
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: 385
Length of database: 382
Length adjustment: 30
Effective length of query: 355
Effective length of database: 352
Effective search space:   124960
Effective search space used:   124960
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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