GapMind for catabolism of small carbon sources

 

Aligments for a candidate for AZOBR_RS08240 in Magnetospirillum magneticum AMB-1

Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate WP_011384209.1 AMB_RS09130 high-affinity branched-chain amino acid ABC transporter permease LivM

Query= uniprot:G8ALI9
         (505 letters)



>lcl|NCBI__GCF_000009985.1:WP_011384209.1 AMB_RS09130 high-affinity
           branched-chain amino acid ABC transporter permease LivM
          Length = 415

 Score =  473 bits (1216), Expect = e-138
 Identities = 256/461 (55%), Positives = 313/461 (67%), Gaps = 57/461 (12%)

Query: 16  SILKEAAMTAFVALLLTIPLVGLRTVDRPTGLGLETRWNEVAAAVGLVFLGRLGLCLIRE 75
           +++ +A +   VA  + +P++G+R  D  TGL L  R + VA A G V   RL + L+R 
Sbjct: 8   ALVVDALLGGVVAAAMALPMLGVRLEDGSTGLSLSGRLDWVAWAAGSVAGARLLIGLLRL 67

Query: 76  GHAVTVLVLAAAATAAGFFIAMPTEALRVILIAGGAVIAIRAVLAIRTGRSKLSQAERDK 135
           G              AG   ++P     +++  G A++A                     
Sbjct: 68  G-------------LAGRGPSLPAPPRAMMVYVGWAMVAF-------------------- 94

Query: 136 RMDHIAAQVQHASRWLGPIAVVVALAFPFTPLADRQLLDIGILLLTYIMLGWGLNIVVGL 195
                                  AL  PF P + R L+D   L+L Y+MLGWGLNIVVGL
Sbjct: 95  -----------------------ALILPFLPFSGRNLVDKATLVLIYVMLGWGLNIVVGL 131

Query: 196 AGLLDLGYVAFYAVGAYSYALLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYF 255
           AGLLDLG+VAFYAVGAYSYALL+  FG SFWVCLPLAG LAA  G++LGFPVLRLRGDY 
Sbjct: 132 AGLLDLGFVAFYAVGAYSYALLSQTFGLSFWVCLPLAGLLAAAFGMVLGFPVLRLRGDYI 191

Query: 256 AIVTLGFGEIIRIILINWYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLE 315
           AIVT+G GEI+R++L NW   TGGPNGISGI RPS FG++ F   P EG+  F E FGL+
Sbjct: 192 AIVTMGLGEIVRVVLQNWQDVTGGPNGISGIERPSLFGLS-FKMVPPEGSQTFAEFFGLD 250

Query: 316 FSPLHRIIFLYYLILVLALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLA 375
           +S  HR+IFLY+LIL LAL+ N+ T+R+R+LP+GRAWEALRED+IAC SLGIN T +KL+
Sbjct: 251 YSADHRVIFLYFLILALALLTNVITLRIRRLPVGRAWEALREDEIACRSLGINPTLVKLS 310

Query: 376 AFAIAAMFGGFAGSFFATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIG 435
           AFA  AMF GFAGSFFATRQGFISPESFTFIESA+ILAIVVLGGMGSQIG+V+AA L++G
Sbjct: 311 AFATGAMFAGFAGSFFATRQGFISPESFTFIESAVILAIVVLGGMGSQIGIVLAALLLVG 370

Query: 436 LPEAFRELADYRMLAFGMGMVLIMLWRPRGLLAHRDPTILL 476
           LPE FREL  +RMLAFG  MVLIMLW+P GLL+ R+PTI L
Sbjct: 371 LPEWFRELQQFRMLAFGGAMVLIMLWKPAGLLSTREPTIRL 411


Lambda     K      H
   0.329    0.144    0.438 

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: 697
Number of extensions: 36
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 505
Length of database: 415
Length adjustment: 33
Effective length of query: 472
Effective length of database: 382
Effective search space:   180304
Effective search space used:   180304
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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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