GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Marinomonas arctica 328

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_111606995.1 DK187_RS08910 ABC transporter ATP-binding protein

Query= TCDB::Q97UF2
         (371 letters)



>NCBI__GCF_003259225.1:WP_111606995.1
          Length = 394

 Score =  213 bits (542), Expect = 7e-60
 Identities = 136/372 (36%), Positives = 210/372 (56%), Gaps = 11/372 (2%)

Query: 1   MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60
           M TI + NL+K +  G TE  +VD VS+T++ G    +LGPSG GKTT LR+IAG+E  T
Sbjct: 1   MPTITLTNLTKCYD-GNTE-PSVDQVSLTVEDGEFMCLLGPSGCGKTTILRMIAGIEHST 58

Query: 61  SGYIYFDNEAVSSPRR-VMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKI 119
           SG I  D+  V S  +   + PEKR I +VFQN+AL+P+MTV  N+ F L+L KVP  + 
Sbjct: 59  SGEIAVDDLVVDSVHQSCFIPPEKRRIGLVFQNYALWPHMTVERNVDFGLRLQKVPAQER 118

Query: 120 ENKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRE 179
           + +  +V  +L +    +RYP +LSGGQ QR A+AR L  +P VLLLDEP SNLDA +R 
Sbjct: 119 KERCVDVMSKLRILEYADRYPSQLSGGQQQRVALARMLAVNPGVLLLDEPLSNLDATLRL 178

Query: 180 SARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLI 239
             RA +R++ +    T + VSHD  +   +AN   V+  G+  QIGTP EIY  P+   +
Sbjct: 179 EMRAELRRLHQTFGTTIIFVSHDQWEAMTLANTIAVMNKGQLQQIGTPDEIYAEPSNRFV 238

Query: 240 ARLTG--EINLIQAKIIENNAIIANLKVPLNNMELKGQSNIVIGLRPDDLTLSDTLLDKY 297
           A   G  +INLI+ K  E+N  + NL   +     + +   V  +RP+++ L+DT     
Sbjct: 239 AEFIGNPKINLIKLK--ESNDELMNLASHILARLPESKFADVCAIRPEEIILTDTANANT 296

Query: 298 IDMGIVKVKLVSYGAGIFKIVVSPITDENIDIIVDAEEPLETGIETHLLAKPNKVKIFDL 357
           + M I  + + + G+ + ++    + ++ +     +      G + +     + +  FD 
Sbjct: 297 LPMNIENI-MPTGGSWVIEL---SLDEDRLFHSTQSRPKWREGEQINAYLPTHSLHFFDH 352

Query: 358 NGSNLITSKTQI 369
           +   L+ S+T +
Sbjct: 353 DEKRLVLSETHL 364


Lambda     K      H
   0.317    0.136    0.374 

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: 293
Number of extensions: 13
Number of successful extensions: 2
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: 371
Length of database: 394
Length adjustment: 30
Effective length of query: 341
Effective length of database: 364
Effective search space:   124124
Effective search space used:   124124
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 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