GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Rhodobacter viridis JA737

Align alpha-ketoglutarate TRAP transporter, large permease component (characterized)
to candidate WP_110805343.1 C8J30_RS08120 TRAP transporter large permease subunit

Query= reanno::SB2B:6938090
         (466 letters)



>NCBI__GCF_003217355.1:WP_110805343.1
          Length = 441

 Score =  160 bits (405), Expect = 8e-44
 Identities = 123/469 (26%), Positives = 218/469 (46%), Gaps = 51/469 (10%)

Query: 4   ATLFLTLFLCMLLGMPIAIALGFSSMLTILLFSNDSLASVALKLYEATSEHYTLLAIPFF 63
           A +F T+ L ML G  +  A+G  +++  L    D    +         +   LL +P F
Sbjct: 8   ALMFSTMLLMMLTGQRVFGAIGIVAVVAALTLWGDGGTDMGFSAVMKLMKWTALLTLPMF 67

Query: 64  ILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIGSIV 123
           +     +S   +A  +       +G + GGLA+ +V+  +L +A++G S A +A   +I 
Sbjct: 68  VFMGYVMSETRLAEDLYRMFHVWMGPLPGGLAIGTVLLMVLISAMNGLSVAGMAIGATIA 127

Query: 124 IVGMVRAGYPQKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPGLLMG 183
           +  + R GY +   +GVI    +LGILIPPS+V+++YA       + +++AG++PGLLM 
Sbjct: 128 LPELQRRGYDKLMISGVIQAGSSLGILIPPSVVLVLYAMIARQPVSNLWLAGIMPGLLMA 187

Query: 184 VLLMVAIYIVARIKNLPSRPFPGVKALSLSSAKAM----GGLALIFIVLGSI---YGGVA 236
            L ++ I I   +    +      +  ++S A+       GL  +FI +  +     G A
Sbjct: 188 ALFILYIIIRTWLNPSLAPRMSAEERAAISRAEKFQLLRAGLLPVFIFVAMMLPFIKGWA 247

Query: 237 SPTEAAAVACVYAYLVAVFGYRDIGPLKEVPWRKEGEAILAAIVRNLLHVGLGLIKTPTD 296
           S TE + V      LVA              W K               +   +++T T 
Sbjct: 248 SLTETSVVGVAATVLVA--------------WAKG-------------RMSWYVLETATK 280

Query: 297 KEIRNVVRDGAKVSIMLLFIIANAMLFAHVL----TTERIPHIIAETIVGWGLPPWGFLI 352
           + +         +++M + II  A+ F  V         I     E +   GL PW  L+
Sbjct: 281 QTL--------LITVMFMMIITAALSFGAVFDGLGAGRSIQTFFTEDL---GLAPWQILV 329

Query: 353 IVNLLLLAAGNFMEPSAILLIMAPILFPIAVQLGIDPIHLGIIMVVNMEIGMLTPPVGLN 412
           ++ +  L  G F++ +A+L+I+AP+   +   LG D I  G++  +  +I  LTPP G N
Sbjct: 330 LMQVSFLIMGMFLDDTAMLVIVAPVYVSLTKALGYDLIWYGVLYTITCQIAYLTPPFGYN 389

Query: 413 LFVTAGIT--GRSIGWVIHACLPWLLLLLGFLVLITYVPQISLFLPEYL 459
           LF+   +     ++  +  +  P++L+++  LVLI   PQI+L+LP+ +
Sbjct: 390 LFLMKALAPPEYTLPVIYRSVWPFVLVMILTLVLIMVFPQIALWLPQVM 438


Lambda     K      H
   0.329    0.144    0.424 

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: 527
Number of extensions: 23
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 466
Length of database: 441
Length adjustment: 33
Effective length of query: 433
Effective length of database: 408
Effective search space:   176664
Effective search space used:   176664
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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