GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c07310 in Rhodococcus qingshengii djl-6-2

Align Inositol transport system permease protein (characterized)
to candidate WP_003940759.1 C1M55_RS10270 ABC transporter permease

Query= reanno::Phaeo:GFF716
         (373 letters)



>NCBI__GCF_002893965.1:WP_003940759.1
          Length = 352

 Score =  216 bits (551), Expect = 6e-61
 Identities = 123/356 (34%), Positives = 189/356 (53%), Gaps = 26/356 (7%)

Query: 11  DERIKTRSKFREAMIRPELGGIIGTITVFAMFLIFAGDSGMFNSQGVMNWSQISAQFMII 70
           DER+K + + +  ++RPE+G ++G I +F  F I A       +   + +S  S+   I+
Sbjct: 17  DERVKEQKRIQRLLLRPEMGSLVGAIAIFIFFCIVAAPFRTPEALATVLYS--SSTIGIM 74

Query: 71  AVGACLLMIAGEFDLSVGSMIGFAGMLIAIFSVTLGWPVWLAILVTFAIATAIGALNGFI 130
           A    LLMI GEFDLS G  +  + +  ++ +  L   +W+  ++   ++ A+G  NG++
Sbjct: 75  ACAVALLMIGGEFDLSAGVAVTTSSLAASMIAYNLHLNLWVGAILALVVSLAVGFFNGYL 134

Query: 131 VVRTGLPSFIVTLAFLFILRGFAIYLPQTIERKTIIGGVADAAEGDWLAALFGGKILTGL 190
           V++T +PSF++TL+   +L G  + + + +  +     V+D A  D        K+    
Sbjct: 135 VMKTKIPSFLITLSSFLMLTGINLAVTKLVSGQVATPSVSDMAGFD-----SAKKVFASS 189

Query: 191 FQWFGDNGWIAVFERGTRKGQPVVEGLPMLIVWAILLVIIGHVILTKTRFGNWIFAAGGD 250
           F  FG +                   + + +VW +L   I   +L KT+ GNWIFA GG+
Sbjct: 190 FSVFGVS-------------------VKITVVWWLLFTAIATFVLFKTKIGNWIFAVGGN 230

Query: 251 AEAARNSGVPVNRVKILMFMFTAFCATVFATCQVMEFGGAGSDRGLLKEFEAIIAVVIGG 310
            ++AR  GVPV  VKI +FM   F A       +  F    S +G+  EF  IIA VIGG
Sbjct: 231 QDSARAIGVPVTAVKIGLFMTVGFAAWFVGMHLLFSFNTVQSGQGVGNEFLYIIAAVIGG 290

Query: 311 ALLTGGYGSVLGAALGALIFGVVQQGLFFAGVESSLFRVFLGLILLFAVILNTYIR 366
            LLTGGYG+ +GAA+GA IFG+  QG+ +AG     F+ FLG +LLFAVI N   R
Sbjct: 291 CLLTGGYGTAIGAAIGAFIFGMTNQGIVYAGWNPDWFKFFLGAMLLFAVIANNAFR 346


Lambda     K      H
   0.330    0.145    0.443 

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: 485
Number of extensions: 33
Number of successful extensions: 3
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: 373
Length of database: 352
Length adjustment: 29
Effective length of query: 344
Effective length of database: 323
Effective search space:   111112
Effective search space used:   111112
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: 49 (23.5 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