GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1750 in Acidovorax sp. GW101-3H11

Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate Ac3H11_2052 Putative glutathione transporter, ATP-binding component

Query= TCDB::Q9X272
         (328 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2052
          Length = 345

 Score =  273 bits (699), Expect = 3e-78
 Identities = 147/334 (44%), Positives = 216/334 (64%), Gaps = 17/334 (5%)

Query: 8   IKMKPLLQTVDLKKYFP------------QGKRILKAVDGISIEIKEGETLGLVGESGCG 55
           +K K L+Q  DL K F             + + +L AVDG+S EI++G+TL LVGESGCG
Sbjct: 14  VKSKALVQAHDLAKTFDVSAPWLNRVIERKPRTLLHAVDGVSFEIEKGKTLALVGESGCG 73

Query: 56  KSTLGRTILKLLRPDGGKIFFEGKDI-TNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVG 114
           KST+ R ++ L  P  G + F+ +D       K+ +  R+++Q+IFQDP  SLNP+  V 
Sbjct: 74  KSTVARLLVGLYEPTRGGLTFDNQDAHAAFKGKDAQAMRRRIQMIFQDPYASLNPRWLVE 133

Query: 115 RIIEDPLIIHKIGTKK-ERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALAL 173
            II +PL  H + T K E + RV ELL  VG+    +  +PH+FSGGQ+QRI IARALA 
Sbjct: 134 DIIGEPLREHGLITDKAELKARVGELLKSVGLSPLDMVKYPHQFSGGQRQRISIARALAT 193

Query: 174 NPKFIVCDEPVSALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLG 233
            P+F+VCDEP SALDVS+QAQ++++++++Q++  ++YLFI+HNLAVV H+S +V VMYLG
Sbjct: 194 EPEFLVCDEPTSALDVSVQAQVLNIMKDLQRERQLTYLFISHNLAVVRHVSDQVGVMYLG 253

Query: 234 KIVEYGDVDKIFLNPIHPYTRALLKSVPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQT 293
           ++VE  D  ++F +P HPYTR LL ++PK+   G+ +    ++GE+P+P++ P GC F  
Sbjct: 254 RLVELADKHQLFNSPRHPYTRMLLDAIPKMHDTGKART--PVQGEVPNPLNPPPGCAFNP 311

Query: 294 RCTEKKAICFEKEPELTEVEKNHFVSCHLVRSYR 327
           RC      C  + P+L  +     ++CH V   R
Sbjct: 312 RCPHVNDRCRTERPKLLSIGGIR-IACHAVEEGR 344


Lambda     K      H
   0.321    0.142    0.417 

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: 357
Number of extensions: 13
Number of successful extensions: 4
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: 328
Length of database: 345
Length adjustment: 28
Effective length of query: 300
Effective length of database: 317
Effective search space:    95100
Effective search space used:    95100
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 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 (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