GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS00885 in Magnetospirillum magneticum AMB-1

Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate WP_043743999.1 AMB_RS09135 branched-chain amino acid ABC transporter permease

Query= uniprot:D8IUY4
         (309 letters)



>lcl|NCBI__GCF_000009985.1:WP_043743999.1 AMB_RS09135 branched-chain
           amino acid ABC transporter permease
          Length = 304

 Score =  251 bits (640), Expect = 2e-71
 Identities = 138/309 (44%), Positives = 195/309 (63%), Gaps = 19/309 (6%)

Query: 1   MDIFIQQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDILMVGAMVGLSLLKVVQQV 60
           M+ F+QQ+INGL LG++Y L+ALGYTMVYGVL +INFAHG I MVGA + L    V   V
Sbjct: 1   MEYFLQQLINGLTLGAIYGLVALGYTMVYGVLGMINFAHGTIYMVGAFISLITFLVATTV 60

Query: 61  APGLPGIVQLVIAIVGAIPVCIVVSLLIERIAYRPLRNAPRLAPLITAIGVSILLQTLAM 120
             G    + LV+ +V A+ +  +     ER+AYRPLR+APRLAPLI+AIGVSI+LQ    
Sbjct: 61  L-GTSVPLALVLTLVAAMALTALWGWTAERVAYRPLRSAPRLAPLISAIGVSIMLQNFVA 119

Query: 121 MIWGRSPLPFPQV-------MPSDPVHIAGALISPTQIMLLALAVLAMVGLVLIVEKTKM 173
              G    P P V       M S    ++   +S  Q++++AL +  M     ++ +T +
Sbjct: 120 QAQGARAKPLPPVFRGGITLMDSGDFVVS---LSWMQMVIMALTLALMAVFTWVITRTAL 176

Query: 174 GRAMRATAENPRIAGLMGVDANKVIVVTFAIGAGLAAIAGVMWAANYSTAQFAMGFVPGL 233
           GRA RA  ++ ++A L+G+D ++VI  TF IGAGLA +AG+M    Y    F +GF+ G+
Sbjct: 177 GRAQRACEQDMKMASLLGIDVDRVISTTFVIGAGLAGVAGMMVTLYYGVIDFYIGFLAGI 236

Query: 234 KAFSAAVLGGIGNIYGAMLGGILLGLIESLGAGYIGDLTGNFLGSNYQDIFAFIVLIIVL 293
           KAF+AAVLGGIG++ GAMLGG+L+GLIE+  + Y            Y+D+  F +L+ VL
Sbjct: 237 KAFTAAVLGGIGSLPGAMLGGLLIGLIEAFWSAY--------FSIEYKDVATFSILVAVL 288

Query: 294 TLRPSGIMG 302
             RP+G++G
Sbjct: 289 VFRPTGLLG 297


Lambda     K      H
   0.328    0.144    0.416 

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: 286
Number of extensions: 8
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: 309
Length of database: 304
Length adjustment: 27
Effective length of query: 282
Effective length of database: 277
Effective search space:    78114
Effective search space used:    78114
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 (21.7 bits)
S2: 48 (23.1 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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