GapMind for catabolism of small carbon sources

 

Alignments 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)



>NCBI__GCF_000009985.1:WP_043743999.1
          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 (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