GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Streptococcus massiliensis 4401825

Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate WP_018372124.1 BN415_RS07505 ABC transporter ATP-binding protein

Query= uniprot:A0A159ZWS6
         (255 letters)



>NCBI__GCF_000341525.1:WP_018372124.1
          Length = 559

 Score =  103 bits (258), Expect = 6e-27
 Identities = 77/252 (30%), Positives = 130/252 (51%), Gaps = 20/252 (7%)

Query: 5   ILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGTILL 64
           +L V++L + +G    + G+ +T+ +KQ +A++G NGAGK+T+   L  F  PT G++  
Sbjct: 296 LLVVKDLRVSYGSQEVLKGIDVTIPKKQRIAIVGKNGAGKSTLAKALCQFV-PTTGSLTW 354

Query: 65  DGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGLFKTPAFR 124
            GE I G      A + +    QN           N +I++     T  F  + K    R
Sbjct: 355 QGEDIAGDSIKERAER-IGYVLQN----------PNQMISE-----TMIFDEVAKGLRLR 398

Query: 125 K-SEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAG 183
             SE E     E  L    L  +   P   L++GQ++R+ IA  ++ RP IL+LDEP AG
Sbjct: 399 GVSESEIEARVEEVLKTCGLHAYRKWPISALSFGQKKRVTIASILVLRPEILLLDEPTAG 458

Query: 184 LNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQIRD 243
            + +   ++   +  L  + + T+++I HDM+L++  SD  +V+  G  +AD +P ++  
Sbjct: 459 QDQRNYTEIMNFLDDLHAKGH-TIIMITHDMQLMLDYSDRALVLVDGQIIADQSPLEVLT 517

Query: 244 NPEVI-KAYLGE 254
           NP ++ KA L E
Sbjct: 518 NPALLAKANLKE 529



 Score = 82.4 bits (202), Expect = 2e-20
 Identities = 64/250 (25%), Positives = 116/250 (46%), Gaps = 25/250 (10%)

Query: 1   MSREILKVENLSMRFGGLL--AVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPT 58
           M + +++ +N S ++       +  + LT+ E + V +IGP+G+GK+T+  CL G     
Sbjct: 1   MKQAMIECKNFSFQYQAQTEPTLKNLDLTIYEGEKVLIIGPSGSGKSTLGQCLNGIIPSI 60

Query: 59  -----GGTILLDGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNF 113
                 G++ + G+    L  +  +             F  +T  E++  A    +    
Sbjct: 61  YPGKQSGSLTIAGQEAFELSIYDKSNLVSTVLQDTDGQFIGLTVAEDVAFALENDVE--- 117

Query: 114 FAGLFKTPAFRKSEREAM-EYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRP 172
                        E   M E    W +K++L          L+ GQ++R+ +A  ++   
Sbjct: 118 -------------ELTTMREKVALWAEKLDLGYLLQHRPQDLSGGQKQRVSLAGVLIDES 164

Query: 173 RILMLDEPAAGLNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVM-SISDHIVVINQGT 231
            IL+ DEP A L+PK  +D+ ALI  L +E   T ++IEH ++ V+    D I++IN+G 
Sbjct: 165 PILLFDEPLANLDPKSGQDIIALIDQLHKEAGTTTIIIEHRLEDVLYRPVDRIILINEGQ 224

Query: 232 PLADGTPEQI 241
            L +GTP+ +
Sbjct: 225 ILFNGTPDAL 234


Lambda     K      H
   0.321    0.138    0.398 

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: 360
Number of extensions: 21
Number of successful extensions: 6
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: 255
Length of database: 559
Length adjustment: 30
Effective length of query: 225
Effective length of database: 529
Effective search space:   119025
Effective search space used:   119025
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: 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